pax_global_header00006660000000000000000000000064124775652450014533gustar00rootroot0000000000000052 comment=ebf75bb000904452d336f6757e282c5813bd68d5 ReadSeq-2.0.2/000077500000000000000000000000001247756524500130605ustar00rootroot00000000000000ReadSeq-2.0.2/.gitignore000066400000000000000000000000531247756524500150460ustar00rootroot00000000000000.svn build dist *~ #*# *tmp* lib/ private/ ReadSeq-2.0.2/LICENSE000066400000000000000000000772461247756524500141050ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. ReadSeq-2.0.2/README000066400000000000000000000012561247756524500137440ustar00rootroot00000000000000Quickstart ========== ant jar java -jar dist/ReadSeq.jar Description ============ Sequence reading library developed by the Ribosomal Database Project. Can handle genbank, embl, fasta, fastq, sff and sto files. Can read from files or streams, and can handle indexing files. USAGE: ReadSeqMain random-sample - random select a subset or subregion of sequences reverse-comp - reverse complement sequences rm-dupseq - remove identical or substring of sequences select-seqs - select or deselect sequences from a file split - split sequences to-fasta - convert to fasta format to-fastq - convert to fastq format ReadSeq-2.0.2/build.xml000066400000000000000000000163051247756524500147060ustar00rootroot00000000000000 Builds, tests, and runs the project ReadSeq. To run this application from the command line without Ant, try: java -jar "${dist.jar.resolved}" ReadSeq-2.0.2/ivy.xml000066400000000000000000000005041247756524500144100ustar00rootroot00000000000000 ReadSeq-2.0.2/manifest.mf000066400000000000000000000001221247756524500152050ustar00rootroot00000000000000Manifest-Version: 1.0 X-COMMENT: Main-Class will be added automatically by build ReadSeq-2.0.2/nbproject/000077500000000000000000000000001247756524500150465ustar00rootroot00000000000000ReadSeq-2.0.2/nbproject/build-impl.xml000066400000000000000000002273611247756524500176410ustar00rootroot00000000000000 Must set src.dir Must set test.src.dir Must set build.dir Must set dist.dir Must set build.classes.dir Must set dist.javadoc.dir Must set build.test.classes.dir Must set build.test.results.dir Must set build.classes.excludes Must set dist.jar Must set javac.includes No tests executed. Must set JVM to use for profiling in profiler.info.jvm Must set profiler agent JVM arguments in profiler.info.jvmargs.agent Must select some files in the IDE or set javac.includes To run this application from the command line without Ant, try: java -jar "${dist.jar.resolved}" Must select one file in the IDE or set run.class Must select one file in the IDE or set run.class Must select one file in the IDE or set debug.class Must select one file in the IDE or set debug.class Must set fix.includes This target only works when run from inside the NetBeans IDE. Must select one file in the IDE or set profile.class This target only works when run from inside the NetBeans IDE. This target only works when run from inside the NetBeans IDE. This target only works when run from inside the NetBeans IDE. Must select one file in the IDE or set run.class Must select some files in the IDE or set test.includes Must select one file in the IDE or set run.class Must select one file in the IDE or set applet.url Must select some files in the IDE or set javac.includes Some tests failed; see details above. Must select some files in the IDE or set test.includes Some tests failed; see details above. Must select some files in the IDE or set test.class Must select some method in the IDE or set test.method Some tests failed; see details above. Must select one file in the IDE or set test.class Must select one file in the IDE or set test.class Must select some method in the IDE or set test.method Must select one file in the IDE or set applet.url Must select one file in the IDE or set applet.url ReadSeq-2.0.2/nbproject/genfiles.properties000066400000000000000000000007231247756524500207620ustar00rootroot00000000000000build.xml.data.CRC32=49286e8a build.xml.script.CRC32=d74ba31a build.xml.stylesheet.CRC32=28e38971@1.50.1.46 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml. # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you. nbproject/build-impl.xml.data.CRC32=8091b603 nbproject/build-impl.xml.script.CRC32=179f1b14 nbproject/build-impl.xml.stylesheet.CRC32=5a01deb7@1.68.1.46 ReadSeq-2.0.2/nbproject/project.properties000066400000000000000000000045671247756524500206460ustar00rootroot00000000000000annotation.processing.enabled=true annotation.processing.enabled.in.editor=false annotation.processing.processors.list= annotation.processing.run.all.processors=true application.title=ReadSeq application.vendor=fishjord build.classes.dir=${build.dir}/classes build.classes.excludes=**/*.java,**/*.form # This directory is removed when the project is cleaned: build.dir=build build.generated.dir=${build.dir}/generated build.generated.sources.dir=${build.dir}/generated-sources # Only compile against the classpath explicitly listed here: build.sysclasspath=ignore build.test.classes.dir=${build.dir}/test/classes build.test.results.dir=${build.dir}/test/results # Uncomment to specify the preferred debugger connection transport: #debug.transport=dt_socket debug.classpath=\ ${run.classpath} debug.test.classpath=\ ${run.test.classpath} # This directory is removed when the project is cleaned: dist.dir=dist dist.jar=${dist.dir}/ReadSeq.jar dist.javadoc.dir=${dist.dir}/javadoc endorsed.classpath= excludes= file.reference.commons-cli-1.2.jar=lib/commons-cli-1.2.jar file.reference.commons-io-2.4.jar=lib/commons-io-2.4.jar file.reference.commons-lang-2.6.jar=lib/commons-lang-2.6.jar file.reference.junit.jar=/scratch/jars/junit.jar includes=** jar.compress=false javac.classpath=\ ${file.reference.commons-cli-1.2.jar}:\ ${file.reference.commons-io-2.4.jar}:\ ${file.reference.commons-lang-2.6.jar} # Space-separated list of extra javac options javac.compilerargs= javac.deprecation=false javac.processorpath=\ ${javac.classpath} javac.source=1.5 javac.target=1.5 javac.test.classpath=\ ${javac.classpath}:\ 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-0.17895503 65140 -8.220582 65141 -7.709757 65142 -6.7542453 65143 -7.373285 65144 -5.822687 65145 -7.12197 65146 -6.7542453 65147 -5.469047 65148 -9.319195 65149 -4.9753895 65150 -6.9212995 65151 -7.12197 65152 -4.109709 65153 -4.724075 65154 -4.7040744 65155 -3.9673367 65156 -6.100319 65157 -4.8305583 65158 -5.655633 65159 -5.17606 65160 -4.2502904 65161 -5.469047 65162 -4.724075 65163 -4.6096644 65164 -5.512532 65165 -4.684466 65166 -6.100319 65167 -4.6278467 65168 -4.5742626 65169 -7.12197 65170 -3.2671056 65171 -5.655633 65172 -5.822687 65173 -6.7542453 65174 -5.655633 65175 -5.763847 65176 -5.17606 65177 -2.825441 65178 -5.7082767 65179 -6.023358 65180 -5.822687 65181 -5.8852077 65182 -4.5570207 65183 -6.6111445 65184 -3.3054795 65185 -4.5742626 65186 -5.2416573 65187 -4.646366 65188 -4.120698 65189 -4.301915 65190 -4.949747 65191 -1.6960417 65192 -3.9579027 65193 -5.4273744 65194 -5.3489027 65195 -2.257003 65196 -7.12197 65197 -1.4971508 65198 -6.374756 65199 -0.37034902 65200 -4.6096644 65201 -5.951899 65202 -5.605623 65203 -6.023358 65204 -1.7238076 65205 -4.646366 65206 -6.9212995 65207 -3.6597126 65208 -4.262949 65209 -7.709757 65210 -6.4859815 65211 -7.12197 65212 -6.1837006 65213 -5.822687 65214 -6.7542453 65215 -6.6111445 65216 -6.2746725 65217 -7.709757 65218 -2.2150507 65219 -0.15962155 65220 -6.7542453 65221 -7.709757 65222 -4.2757697 65223 -6.9212995 65224 -2.9788353 65225 -7.709757 65226 -7.373285 65227 -4.6278467 65228 -0.1625717 65229 -6.6111445 65230 -7.12197 65231 -6.374756 65232 -6.100319 65233 -6.6111445 65234 -6.7542453 65235 -7.373285 65236 -6.6111445 65237 -6.023358 65238 -5.763847 65239 -6.1837006 65240 -4.8305583 65241 -5.605623 65242 -6.023358 65243 -7.373285 65244 -7.12197 65245 -5.763847 65246 -7.709757 65247 -6.7542453 65248 -4.744484 65249 -5.557995 65250 -2.5179117 65251 -6.023358 65252 -4.3152485 65253 -3.1433275 65254 -4.428846 65255 -2.4915655 65256 -6.9212995 65257 -3.5050642 65258 -9.319195 65259 -1.8512524 65260 -6.374756 65261 -4.4439974 65262 -9.319195 65263 -4.4593825 65264 -6.374756 65265 -7.373285 65266 -7.373285 65267 -5.951899 65268 -5.951899 65269 -6.374756 65270 -1.2848879 65271 -5.655633 65272 -5.951899 65273 -5.512532 65274 -6.1837006 65275 -6.374756 65276 -6.1837006 65277 -6.6111445 65278 -6.7542453 65279 -5.512532 65280 -4.120698 65281 -5.3489027 65282 -4.3704348 65283 -5.763847 65284 -7.373285 65285 -7.373285 65286 -5.557995 65287 -9.319195 65288 -6.1837006 65289 -4.6278467 65290 -4.8532867 65291 -4.213249 65292 -8.220582 65293 -7.709757 65294 -6.2746725 65295 -5.763847 65296 -4.8765435 65297 -5.8852077 65298 -4.9753895 65299 -5.028735 65300 -7.709757 65301 -7.709757 65302 -8.220582 65303 -8.220582 65304 -2.2484705 65305 -5.7082767 65306 -6.023358 65307 -5.387369 65308 -6.6111445 65309 -6.374756 65310 -7.709757 65311 -5.0017066 65312 -5.387369 65313 -8.220582 65314 -4.8532867 65315 -5.114502 65316 -5.3118615 65317 -3.560293 65318 -5.7082767 65319 -7.373285 65320 -6.1837006 65321 -9.319195 65322 -7.373285 65323 -6.1837006 65324 -6.2746725 65325 -5.951899 65326 -8.220582 65327 -6.374756 65328 -5.822687 65329 -4.41392 65330 -7.373285 65331 -3.7779312 65332 -8.220582 65333 -6.7542453 65334 -8.220582 65335 -5.0565147 65336 -5.7082767 65337 -9.319195 65338 -6.1837006 65339 -9.319195 65340 -7.373285 65341 -6.7542453 65342 -7.12197 65343 -7.373285 65344 -6.374756 65345 -5.951899 65346 -6.4859815 65347 -6.4859815 65348 -6.6111445 65349 -3.3006015 65350 -5.557995 65351 -3.1516783 65352 -5.512532 65353 -5.512532 65354 -5.763847 65355 -5.512532 65356 -5.8852077 65357 -5.208321 65358 -5.512532 65359 -4.8083353 65360 -5.557995 65361 -0.8717805 65362 -3.441459 65363 -4.213249 65364 -7.373285 65365 -4.9753895 65366 -5.3489027 65367 -4.213249 65368 -6.023358 65369 -2.63084 65370 -3.6322193 65371 -6.374756 65372 -5.605623 65373 -4.328762 65374 -2.9894738 65375 -5.1448073 65376 -5.2761436 65377 -6.374756 65378 -5.763847 65379 -3.1901445 65380 -5.2416573 65381 -4.02589 65382 -5.208321 65383 -3.8596091 65384 -2.2812889 65385 -5.557995 65386 -3.2577379 65387 -5.0850883 65388 -5.3118615 65389 -5.2416573 65390 -5.951899 65391 -4.2502904 65392 -9.319195 65393 -8.220582 65394 -5.028735 65395 -5.8852077 65396 -6.2746725 65397 -6.100319 65398 -6.7542453 65399 -5.028735 65400 -6.7542453 65401 -5.763847 65402 -5.2416573 65403 -6.374756 65404 -5.822687 65405 -5.3118615 65406 -7.12197 65407 -6.7542453 65408 -5.655633 65409 -6.7542453 65410 -5.822687 65411 -6.9212995 65412 -8.220582 65413 -6.1837006 65414 -5.8852077 65415 -8.220582 65416 -5.208321 65417 -5.763847 65418 -5.3489027 65419 -3.9030943 65420 -7.709757 65421 -5.1448073 65422 -5.951899 65423 -8.220582 65424 -4.35635 65425 -6.100319 65426 -6.9212995 65427 -6.023358 65428 -7.373285 65429 -3.9579027 65430 -6.4859815 65431 -7.709757 65432 -2.676708 65433 -5.512532 65434 -7.709757 65435 -6.4859815 65436 -6.023358 65437 -7.12197 65438 -7.12197 65439 -5.028735 65440 -3.7319462 65441 -5.3489027 65442 -5.951899 65443 -5.3489027 65444 -3.2392616 65445 -5.114502 65446 -6.1837006 65447 -6.374756 65448 -3.9579027 65449 -3.5666223 65450 -5.951899 65451 -1.6390191 65452 -5.557995 65453 -1.6216195 65454 -6.6111445 65455 -6.2746725 65456 -3.4641228 65457 -5.655633 65458 -6.7542453 65459 -4.342461 65460 -6.7542453 65461 -6.100319 65462 -7.373285 65463 -7.12197 65464 -4.399214 65465 -5.7082767 65466 -4.744484 65467 -4.744484 65468 -7.12197 65469 -1.5807067 65470 -5.605623 65471 -6.4859815 65472 -6.374756 65473 -9.319195 65474 -5.3489027 65475 -6.2746725 65476 -7.709757 65477 -8.220582 65478 -5.4273744 65479 -6.374756 65480 -5.8852077 65481 -4.8532867 65482 -6.7542453 65483 -5.763847 65484 -3.295747 65485 -6.374756 65486 -7.709757 65487 -6.6111445 65488 -7.12197 65489 -9.319195 65490 -9.319195 65491 -7.373285 65492 -7.709757 65493 -5.655633 65494 -3.014746 65495 -5.3118615 65496 -5.557995 65497 -5.951899 65498 -2.0586722 65499 -7.373285 65500 -6.7542453 65501 -7.12197 65502 -5.655633 65503 -6.2746725 65504 -6.7542453 65505 -6.7542453 65506 -5.951899 65507 -5.3489027 65508 -7.373285 65509 -7.709757 65510 -6.1837006 65511 -4.8765435 65512 -5.8852077 65513 -6.374756 65514 -5.512532 65515 -3.5729916 65516 -5.387369 65517 -7.709757 65518 -5.028735 65519 -5.605623 65520 -6.9212995 65521 -7.709757 65522 -6.023358 65523 -6.100319 65524 -9.319195 65525 -3.9961848 65526 -5.8852077 65527 -5.8852077 65528 -6.100319 65529 -6.4859815 65530 -6.4859815 65531 -6.374756 65532 -6.374756 65533 -7.709757 65534 -6.9212995 65535 -6.9212995 ReadSeq-2.0.2/src/data/protein_coding_tables.txt000066400000000000000000000371171247756524500216670ustar00rootroot00000000000000transl_table=1 The Standard Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA * Ter TTG L Leu i TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu i CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=2 The Vertebrate Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA W Trp TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile i ACT T Thr AAT N Asn AGT S Ser ATC I Ile i ACC T Thr AAC N Asn AGC S Ser ATA M Met i ACA T Thr AAA K Lys AGA * Ter ATG M Met i ACG T Thr AAG K Lys AGG * Ter GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=3 The Yeast Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA W Trp TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT T Thr CCT P Pro CAT H His CGT R Arg CTC T Thr CCC P Pro CAC H His CGC R Arg CTA T Thr CCA P Pro CAA Q Gln CGA R Arg CTG T Thr CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA M Met i ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=4 The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu i TCA S Ser TAA * Ter TGA W Trp TTG L Leu i TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu i CCG P Pro CAG Q Gln CGG R Arg ATT I Ile i ACT T Thr AAT N Asn AGT S Ser ATC I Ile i ACC T Thr AAC N Asn AGC S Ser ATA I Ile i ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=5 The Invertebrate Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA W Trp TTG L Leu i TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile i ACT T Thr AAT N Asn AGT S Ser ATC I Ile i ACC T Thr AAC N Asn AGC S Ser ATA M Met i ACA T Thr AAA K Lys AGA S Ser ATG M Met i ACG T Thr AAG K Lys AGG S Ser GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=6 The Ciliate, Dasycladacean and Hexamita Nuclear Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA Q Gln TGA * Ter TTG L Leu TCG S Ser TAG Q Gln TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=9 The Echinoderm and Flatworm Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA W Trp TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA N Asn AGA S Ser ATG M Met i ACG T Thr AAG K Lys AGG S Ser GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=10 The Euplotid Nuclear Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA C Cys TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=11 The Bacterial, Archaeal and Plant Plastid Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA * Ter TTG L Leu i TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu i CCG P Pro CAG Q Gln CGG R Arg ATT I Ile i ACT T Thr AAT N Asn AGT S Ser ATC I Ile i ACC T Thr AAC N Asn AGC S Ser ATA I Ile i ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=12 The Alternative Yeast Nuclear Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA * Ter TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG S Ser i CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=13 The Ascidian Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA W Trp TTG L Leu i TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA M Met i ACA T Thr AAA K Lys AGA G Gly ATG M Met i ACG T Thr AAG K Lys AGG G Gly GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=14 The Alternative Flatworm Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA Y Tyr TGA W Trp TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA N Asn AGA S Ser ATG M Met i ACG T Thr AAG K Lys AGG S Ser GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=15 Blepharisma Nuclear Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA * Ter TTG L Leu TCG S Ser TAG Q Gln TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=16 Chlorophycean Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA * Ter TTG L Leu TCG S Ser TAG L Leu TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=21 Trematode Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Ter TGA W Trp TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA M Met ACA T Thr AAA N Asn AGA S Ser ATG M Met i ACG T Thr AAG K Lys AGG S Ser GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly transl_table=22 Scenedesmus obliquus mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA * Ter TAA * Ter TGA * Ter TTG L Leu TCG S Ser TAG L Leu TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly transl_table=23 Thraustochytrium Mitochondrial Code TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA * Ter TCA S Ser TAA * Ter TGA * Ter TTG L Leu TCG S Ser TAG * Ter TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile i ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met i ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val i GCG A Ala GAG E Glu GGG G Gly ReadSeq-2.0.2/src/data/ref_seqs.fa000066400000000000000000000060741247756524500167060ustar00rootroot00000000000000>RDPX-Bacteria Escherichia coli (J01695) AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGgtaacaggaagaagcttgcttctttgctgacgAGTGGCGGACGGGTGAGTAATGTCTGGGA-AACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAAC-------GTCGCAAGAC-------CAAAGAgggggaccttcgggcctcTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAagggagtaaagttaatacctttgctcatTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGcccttgaggCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATgtgccttcgggaaCCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGgtccggcCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTagcttaaccttcgggagggcGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA >RDPX-Archaea Methanocaldococcus jannaschii (L77117) ATTCCGGTTGATCCTGCCGGAGGCCACTGCTATCGGGGTCCGACTAAGCCATGCGAGTCAaGGGgctcccttcggggagcACCGGCGCACGGCTCAGTAACACGTGGCTAACCTACCCTCGGGTGGGGGATAACCTCGGGAAACTGAGGCTAATCCCCCATAGGGGAGGAGGTCTGGAATGATCCCTCCCCGAAAGGCgtaaGCCGCCCGAGGATGGGGCTGCGGCGGATTAGGTAGTTGGTGGGGTAACGGCCCACCAAGCCTACGATCCGTACGGGCCCTGAGAGGGGGAGCCCGGAGATGGACACTGAGACACGGGTCCAGGCCcTACGGGGCGCAGCAGGCGCGAAACCTCCGCAATGCGCGAAAGCGCGACGGGGGGACCCCGAGTGCCcaCGCCCTGCGtgGGCTTTTCCGGAGTGTAAACAGCTCCGGGAATAAGGGCTGGGCAAGTCCGGTGCCAGCAGCCGCGGTAATACCGGCGGCCCAAGTGGTGGCCACTGTTATTGGGCCTAAAGCGTCCGTAGCCGGCCCGGTAAGTCTCTGCTTAAATCCTGCGGCTCAACCGCAGGGCTGGCAGAGATACTGCCGGGCTTGGGACCGGGAGAGGCCGGGGGTACCCCAGGGGTAGCGGTGAAATGCGTTGATCCCTGGGGGACCACCTGTGGCGAAGGCGCCCGGCTGGAACGGGTCCGACGGTGAGGGACGAAGGCCAGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACTCTGCGGACTAGGTGTCGCGTCGGCTTCGGGCCGACGCGGTGCCGAAGGGAAGCCGTTAAGTCCGCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTTAAAGGAATTGGCGGGGGAGCACTACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGCATCTTACCAGGGGCGACGGCAGGATGAAGGCCAGGTTGACGACCTTGCCAGACGCGCCGAGAGGTGGTGCATGGCCGTCGTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTCAGGTAACGAGCGAGACCCGTGCCCCATGTTGCTACCTCCTCCTCCgGGAGGAGGGCACTCATGGGGGACCGCCGGCGcTAAGCCGGAGGAAGGTGCGGGCAACGACAGGTCCGCATGCCCCGAATCCCCTGGGCTACACGCGGGCTACAATGGCCGGGACAATGGGACGCGACCCCGAAAGGGGGAGCGAATCCCCtAAACCCGGTCGTAGTCCGGATCGAGGGCTGTAACTCGCCCTCGTGAAGCCGGAATCCGTAGTAATCGCGCCTCACCATGGCGCGGTGAATGCGTCCCTGCTCCTTGCACACACCGCCCGTCACGCCACCCGAGTTGAGcCCAAGTGAGGCCCTGTCCGcaAGGGCAGGGTCGAACTTGGgTTCAGCGAGGGGGGCGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCReadSeq-2.0.2/src/edu/000077500000000000000000000000001247756524500144245ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/000077500000000000000000000000001247756524500152305ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/000077500000000000000000000000001247756524500157745ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/000077500000000000000000000000001247756524500165615ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/000077500000000000000000000000001247756524500202055ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/MaskSequenceNotFoundException.java000066400000000000000000000017441247756524500267760ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; /** * * @author fishjord */ public class MaskSequenceNotFoundException extends Exception { public MaskSequenceNotFoundException(String maskSeqId) { super("Failed to find mask sequence \"" + maskSeqId + "\" in sequence file"); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/QSequence.java000066400000000000000000000014171247756524500227440ustar00rootroot00000000000000/* * Sequence.java * * Copyright 2006 Michigan State University Board of Trustees * * Created on November 7, 2003, 5:41 PM */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.Sequence; /** * An abstract class, providing an interface for accessing a sequence. * @author wangqion, fishjord */ public class QSequence extends Sequence{ protected byte[] quality; public QSequence(String seqName, String desc, String seqString, byte[] quality) { super(seqName, desc, seqString); this.quality = quality; } public QSequence(Sequence s, byte[] quality) { super(s.getSeqName(), s.getDesc(), s.getSeqString()); this.quality = quality; } public byte[] getQuality() { return quality; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/ReadSeqMain.java000066400000000000000000000054771247756524500232160ustar00rootroot00000000000000/* * Copyright (C) 2014 wangqion * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.utils.ResampleSeqFile; import edu.msu.cme.rdp.readseq.utils.RevComplement; import edu.msu.cme.rdp.readseq.utils.RmDupSeqs; import edu.msu.cme.rdp.readseq.utils.SeqFileSplitter; import edu.msu.cme.rdp.readseq.utils.SequenceSelector; import edu.msu.cme.rdp.readseq.writers.StkWriter; import java.util.Arrays; /** * * @author wangqion */ public class ReadSeqMain { public static void main(String [] args) throws Exception { String usage = "USAGE: ReadSeqMain " + "\n\trandom-sample - random select a subset or subregion of sequences" + "\n\treverse-comp - reverse complement sequences" + "\n\trm-dupseq - remove identical or substring of sequences" + "\n\tselect-seqs - select or deselect sequences from a file" + "\n\tsplit - split sequences" + "\n\tto-fasta - convert to fasta format" + "\n\tto-fastq - convert to fastq format" + "\n\tto-stk - convert to stk format" ; if(args.length == 0 ) { System.err.println(usage); return; } String cmd = args[0]; String[] newArgs = Arrays.copyOfRange(args, 1, args.length); if(cmd.equals("select-seqs")) { SequenceSelector.main(newArgs); }else if(cmd.equals("random-sample")) { ResampleSeqFile.main(newArgs); }else if(cmd.equals("reverse-comp")) { RevComplement.main(newArgs); }else if(cmd.equals("rm-dupseq")) { RmDupSeqs.main(newArgs); }else if(cmd.equals("to-fasta")) { ToFasta.main(newArgs); }else if(cmd.equals("to-fastq")) { ToFastq.main(newArgs); }else if(cmd.equals("to-stk")) { StkWriter.main(newArgs); }else if(cmd.equals("split")) { SeqFileSplitter.main(newArgs); } else { System.err.println("ERROR: " + "wrong subcommand"); System.err.println(usage); return; } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/SeqFactory.java000066400000000000000000000022571247756524500231360ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.Sequence; /** * * @author fishjord */ public abstract class SeqFactory { public static final SeqFactory defaultFactory = new SeqFactory() { public Sequence buildSequence(String seqName, String desc, String seqString) { return new Sequence(seqName, desc, seqString); } }; public abstract E buildSequence(String seqName, String desc, String seqString); } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/SeqTrunc.java000066400000000000000000000047271247756524500226260ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import java.io.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; /** * * @author fishjord */ public class SeqTrunc { public static void main(String[] args) throws IOException { if(args.length != 2) { System.err.println("USAGE: SeqTrunc "); System.exit(1); } File seqFile = new File(args[0]); int truncLen = Integer.parseInt(args[1]); FastaWriter out = new FastaWriter(new BufferedOutputStream(new FileOutputStream("trunc_seqs.fasta"))); int[] lengthHisto = new int[255]; Sequence seq; SeqReader reader = new SequenceReader(seqFile); while((seq = reader.readNextSequence()) != null) { String seqString = seq.getSeqString(); int seqLength = seqString.length(); if(seqLength > truncLen) { seqString = seqString.substring(0, truncLen); } lengthHisto[seqLength]++; out.writeSeq(seq.getSeqName(), seq.getDesc(), seqString); } out.close(); int count = 0; int tot = 0; for(int index = 0;index < lengthHisto.length;index++) { tot += lengthHisto[index] * index; count += lengthHisto[index]; if(lengthHisto[index] > 0) { System.err.println(index + "\t" + lengthHisto[index]); } } System.err.println("Total sequences: " + count + ", average length: " + ((float)tot / count)); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/SequenceFormat.java000066400000000000000000000015721247756524500237760ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; /** * * @author fishjord */ public enum SequenceFormat { FASTA, FASTQ, STK, GENBANK, EMBL, UNKNOWN, SFF, SRF, EMPTY, IN_MEMORY, GZIP }; ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/SequenceParsingException.java000066400000000000000000000012051247756524500260210ustar00rootroot00000000000000/* * SequenceParsingException.java * * Copyright 2006 Michigan State University Board of Trustees * * Created on November 7, 2003, 5:47 PM */ package edu.msu.cme.rdp.readseq; /** * A class to handle the exception during sequence parsing. * @author wangqion */ public class SequenceParsingException extends Exception { private int lineno; /** * Creates a new instance of SequenceParsingException with detail message. */ public SequenceParsingException(String msg, int lineno) { super(msg); this.lineno = lineno; } public int getLineno() { return lineno; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/SequenceType.java000066400000000000000000000015101247756524500234570ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; /** * * @author fishjord */ public enum SequenceType { Nucleotide, Protein, Unknown } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/ToFasta.java000066400000000000000000000066371247756524500224250ustar00rootroot00000000000000/* * Copyright (C) 2013 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import java.io.File; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; /** * * @author Jordan Fish */ public class ToFasta { public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption("m", "mask", true, "Mask sequence name indicating columns to drop"); String maskSeqid = null; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("mask")) { maskSeqid = line.getOptionValue("mask"); } args = line.getArgs(); if ( args.length == 0){ throw new Exception(""); } } catch (Exception e) { new HelpFormatter().printHelp("USAGE: to-fasta ", options); System.err.println("ERROR: " + e.getMessage()); System.exit(1); return; } SeqReader reader = null; FastaWriter out = new FastaWriter(System.out); Sequence seq; int totalSeqs = 0; long totalTime = System.currentTimeMillis(); for (String fname : args) { if (fname.equals("-")) { reader = new SequenceReader(System.in); } else { File seqFile = new File(fname); if (maskSeqid == null) { reader = new SequenceReader(seqFile); } else { reader = new IndexedSeqReader(seqFile, maskSeqid); } } long startTime = System.currentTimeMillis(); int thisFileTotalSeqs = 0; while ((seq = reader.readNextSequence()) != null) { out.writeSeq(seq.getSeqName().replace(" ", "_"), seq.getDesc(), seq.getSeqString()); thisFileTotalSeqs++; } totalSeqs += thisFileTotalSeqs; System.err.println("Converted " + thisFileTotalSeqs + " (total sequences: " + totalSeqs + ") sequences from " + fname + " (" + reader.getFormat() + ") to fasta in " + (System.currentTimeMillis() - startTime) / 1000 + " s"); } System.err.println("Converted " + totalSeqs + " to fasta in " + (System.currentTimeMillis() - totalTime) / 1000 + " s"); out.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/ToFastq.java000066400000000000000000000045121247756524500224330ustar00rootroot00000000000000/* * Copyright (C) 2013 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import edu.msu.cme.rdp.readseq.readers.QSeqReader; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.writers.FastqWriter; import java.io.File; import java.io.IOException; /** * * @author Jordan Fish */ public class ToFastq { public static void main(String[] args) throws Exception { if (args.length != 1 && args.length != 2) { System.err.println("USAGE: ToFastq [qualfile]"); System.exit(1); } final SeqReader reader; if (args.length == 2) { reader = new QSeqReader(new File(args[0]), new File(args[1])); } else { reader = new SequenceReader(new File(args[0])); } Sequence seq = reader.readNextSequence(); if (!(seq instanceof QSequence)) { throw new IOException("Input doesn't contain quality information"); } FastqWriter out = new FastqWriter(System.out, FastqCore.Phred33QualFunction); long startTime = System.currentTimeMillis(); int thisFileTotalSeqs = 0; do { out.writeSeq(seq); thisFileTotalSeqs++; } while ((seq = reader.readNextSequence()) != null); System.err.println("Converted " + thisFileTotalSeqs + " sequences (" + reader.getFormat() + ") to fastq in " + (System.currentTimeMillis() - startTime) / 1000 + " s"); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/000077500000000000000000000000001247756524500216325ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/BufferedLineReader.java000066400000000000000000000041711247756524500261550ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.Reader; /** * * @author fishjord */ public class BufferedLineReader { private BufferedReader reader; private String peekBuffer = null; private int lineno = 0; public BufferedLineReader(InputStream is) { reader = new BufferedReader(new InputStreamReader(is)); } public BufferedLineReader(File f) throws IOException { reader = new BufferedReader(new FileReader(f)); } public BufferedLineReader(Reader reader) { if(reader instanceof BufferedReader) this.reader = (BufferedReader)reader; else this.reader = new BufferedReader(reader); } public String readLine() throws IOException { String ret; if(peekBuffer != null) { ret = peekBuffer; peekBuffer = null; } else ret = reader.readLine(); if(ret != null) lineno++; return ret; } public String peek() throws IOException { if(peekBuffer == null) { peekBuffer = readLine(); } return peekBuffer; } public int getLineno() { return lineno; } public void close() throws IOException { reader.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/IndexedSeqReader.java000066400000000000000000000306121247756524500256530ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.MaskSequenceNotFoundException; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.readers.core.EMBLCore; import edu.msu.cme.rdp.readseq.readers.core.FastaCore; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.readers.core.GenbankCore; import edu.msu.cme.rdp.readseq.readers.core.SeqReaderCore; import edu.msu.cme.rdp.readseq.readers.core.SFFCore; import edu.msu.cme.rdp.readseq.readers.core.STKCore; import edu.msu.cme.rdp.readseq.readers.core.SeqReaderCore.EmptyCore; import edu.msu.cme.rdp.readseq.utils.SeqUtils; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.DataInputStream; import java.io.DataOutputStream; import java.io.EOFException; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Set; import java.util.concurrent.locks.ReentrantLock; /** * * @author fishjord */ public class IndexedSeqReader implements SeqReader { public Map seqIndex = new LinkedHashMap(); private boolean ignoreGaps = false; private boolean filterSeqs = false; private static ReentrantLock lock = new ReentrantLock(); private char[] maskSeq; private SeqReaderCore core; private SequenceFormat format; public IndexedSeqReader(File f) throws IOException { setup(f, false, true, null, SeqUtils.guessFileFormat(f)); } public IndexedSeqReader(File f, boolean ignoreGaps) throws IOException { setup(f, ignoreGaps, true, null, SeqUtils.guessFileFormat(f)); } public IndexedSeqReader(File f, File indexFile) throws IOException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, false, true, readExternalIndex(f, indexFile, guess), guess); } public IndexedSeqReader(File f, File indexFile, boolean ignoreGaps) throws IOException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, ignoreGaps, true, readExternalIndex(f, indexFile, guess), guess); } public IndexedSeqReader(File f, File indexFile, String maskSeqId) throws IOException, MaskSequenceNotFoundException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, maskSeqId, false, true, readExternalIndex(f, indexFile, guess), guess); } public IndexedSeqReader(File f, File indexFile, String maskSeqId, boolean ignoreGaps) throws IOException, MaskSequenceNotFoundException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, maskSeqId, ignoreGaps, true, readExternalIndex(f, indexFile, guess), guess); } public IndexedSeqReader(File f, String maskSeqId) throws IOException, MaskSequenceNotFoundException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, maskSeqId, false, true, null, guess); } public IndexedSeqReader(File f, String maskSeqId, boolean ignoreGaps) throws IOException, MaskSequenceNotFoundException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, maskSeqId, ignoreGaps, true, null, guess); } public IndexedSeqReader(File f, boolean ignoreGaps, boolean filterSeqs) throws IOException { setup(f, ignoreGaps, filterSeqs, null, SeqUtils.guessFileFormat(f)); } public IndexedSeqReader(File f, File indexFile, boolean ignoreGaps, boolean filterSeqs) throws IOException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, ignoreGaps, filterSeqs, readExternalIndex(f, indexFile, guess), guess); } public IndexedSeqReader(File f, File indexFile, String maskSeqId, boolean ignoreGaps, boolean filterSeqs) throws IOException, MaskSequenceNotFoundException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, maskSeqId, ignoreGaps, filterSeqs, readExternalIndex(f, indexFile, guess), guess); } public IndexedSeqReader(File f, String maskSeqId, boolean ignoreGaps, boolean filterSeqs) throws IOException, MaskSequenceNotFoundException { SequenceFormat guess = SeqUtils.guessFileFormat(f); setup(f, maskSeqId, ignoreGaps, filterSeqs, null, guess); } private void setup(File seqFile, String maskSeqId, boolean ignoreGaps, boolean filterSeqs, Map suppliedSeqIndex, SequenceFormat format) throws IOException, MaskSequenceNotFoundException { setup(seqFile, ignoreGaps, filterSeqs, suppliedSeqIndex, format); if (!seqIndex.containsKey(maskSeqId)) { throw new MaskSequenceNotFoundException(maskSeqId); } Sequence seq = core.parse(seqIndex.get(maskSeqId)); maskSeq = SeqUtils.filterSeqString(seq.getSeqString(), false).toCharArray(); core.seek(seqIndex.get(getSeqIds().get(0))); } private void setup(File seqFile, boolean ignoreGaps, boolean filterSeqs, Map suppliedSeqIndex, SequenceFormat format) throws IOException { if (format == SequenceFormat.FASTA) { core = new FastaCore(seqFile); } else if (format == SequenceFormat.FASTQ) { core = new FastqCore(seqFile); } else if (format == SequenceFormat.SFF) { core = new SFFCore(seqFile); } else if (format == SequenceFormat.STK) { core = new STKCore(seqFile); } else if (format == SequenceFormat.EMBL) { core = new EMBLCore(seqFile); } else if (format == SequenceFormat.GENBANK) { core = new GenbankCore(seqFile); } else if (format == SequenceFormat.EMPTY) { core = new EmptyCore(seqFile); } else { throw new IOException("Unsupported file format " + format); } this.ignoreGaps = ignoreGaps; this.filterSeqs = filterSeqs; this.format = format; if (suppliedSeqIndex == null) { suppliedSeqIndex = core.scan(); } this.seqIndex = suppliedSeqIndex; } public SequenceFormat getFormat() { return format; } public static List readFully(File seqFile, String maskSeq, boolean ignoreGaps, boolean filterSeqs) throws IOException, MaskSequenceNotFoundException { List ret = new ArrayList(); IndexedSeqReader reader = new IndexedSeqReader(seqFile, maskSeq, ignoreGaps, filterSeqs); try { for (String seqid : reader.getSeqIdSet()) { if (seqid.startsWith("#")) { continue; } ret.add(reader.readSeq(seqid)); } return ret; } finally { reader.close(); } } private static Map readExternalIndex(File seqFile, File indexFile, SequenceFormat expectedFormat) throws IOException { DataInputStream reader = new DataInputStream(new BufferedInputStream(new FileInputStream(indexFile))); if (reader.readLong() != seqFile.length()) { throw new IOException("Sequence file's size has changed since it was index"); } SequenceFormat format = SequenceFormat.valueOf(reader.readUTF()); if (format != expectedFormat) { throw new IllegalArgumentException("Sequence file format " + format + " is not of the expected format " + expectedFormat); } Map ret = new HashMap(); while (true) { try { String seqid = reader.readUTF(); Long index = reader.readLong(); ret.put(seqid, index); } catch (EOFException e) { break; } } reader.close(); return ret; } public static void indexSeqFile(File seqFile, File indexFile) throws IOException { indexSeqFile(seqFile, indexFile, SeqUtils.guessFileFormat(seqFile)); } public static void indexSeqFile(File seqFile, File indexFile, SequenceFormat format) throws IOException { FastaCore core; if (format == SequenceFormat.FASTA) { core = new FastaCore(seqFile); } else { throw new IllegalArgumentException("Format " + format + "is not supported"); } DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(indexFile))); long startTime = System.currentTimeMillis(); int written = core.scanToStream(out); System.out.println("Indexed " + written + " sequences in " + (System.currentTimeMillis() - startTime) + " ms"); } public void close() throws IOException { core.close(); } public List getSeqIds() { List ret = new ArrayList(seqIndex.keySet()); //XXX Hack to prevent meta-sequences from being returned with the list Set remove = new HashSet(Arrays.asList("struct", "structure", "mask")); for (String seqid : ret) { if (seqid.startsWith("#")) { remove.add(seqid); } } ret.removeAll(remove); return ret; } public Set getSeqIdSet() { return Collections.unmodifiableSet(seqIndex.keySet()); } private Sequence readFrom(long location) throws IOException { Sequence seq = core.parse(location); try { if (filterSeqs && seq.getSeqName() != null) { seq.setSeqString(filterSequence(seq.getSeqString())); } return seq; } catch (Exception e) { throw new RuntimeException("Failed to filter sequence " + seq.getSeqName(), e); } } public Sequence readSeq(String id) throws IOException { try { lock.lock(); if (seqIndex.containsKey(id)) { return readFrom(seqIndex.get(id)); } else { throw new IOException("Sequence " + id + " not found in file"); } } finally { lock.unlock(); } } public List readSeqs(Collection ids) throws IOException { List ret = new ArrayList(); for (String id : ids) { ret.add(readSeq(id)); } return ret; } public Sequence readNextSequence() throws IOException { try { lock.lock(); Sequence seq = core.readNextSequence(); try { if (filterSeqs && seq != null && seq.getSeqName() != null) { seq.setSeqString(filterSequence(seq.getSeqString())); } return seq; } catch (Exception e) { throw new RuntimeException("Failed to filter sequence " + seq.getSeqName(), e); } } finally { lock.unlock(); } } protected String filterSequence(String seq) { seq = SeqUtils.filterSeqString(seq, ignoreGaps); if (maskSeq != null) { seq = SeqUtils.getMaskedSeq(seq, maskSeq); } return seq; } public static void main(String[] args) throws Exception { long startTime = System.currentTimeMillis(); IndexedSeqReader reader = new IndexedSeqReader(new File("/scratch/fishjord/woojun_unifrac_run3/run3.fasta")); long stopTime = System.currentTimeMillis(); System.out.println("Time to index file: " + (stopTime - startTime) + "ms"); System.out.println("Mask seq index: " + reader.seqIndex.get("#=GC_SS_cons")); System.out.println("Mask seq: " + reader.readSeq("#=GC_SS_cons").getSeqString()); System.out.println("Total seq count: " + reader.getSeqIds().size()); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/MemSeqReader.java000066400000000000000000000033551247756524500250150ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.SequenceFormat; import java.io.IOException; import java.util.Arrays; import java.util.Collection; import java.util.Iterator; /** * * @author fishjord */ public class MemSeqReader implements SeqReader { private Iterator seqs; public MemSeqReader(Iterator seqs) { this.seqs = seqs; } public MemSeqReader(Collection seqs) { this(seqs.iterator()); } public MemSeqReader(E ... seqs) { this.seqs = Arrays.asList(seqs).iterator(); } public E readNextSequence() throws IOException { if(seqs != null && seqs.hasNext()) { return seqs.next(); } return null; } public SequenceFormat getFormat() { return SequenceFormat.IN_MEMORY; } public void close() throws IOException { seqs = null; //We can't really 'close' an in memory sequence reader, but we can //indicate to the jvm that the backing sequences can be gc'ed } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/MultiFileSeqReader.java000066400000000000000000000043311247756524500261640ustar00rootroot00000000000000/* * Copyright (C) 2013 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.SequenceFormat; import java.io.File; import java.io.IOException; import java.util.List; /** * * @author Jordan Fish */ public class MultiFileSeqReader implements SeqReader { private final List inputFiles; private SeqReader currReader; private int seqFileIndex; public MultiFileSeqReader(List inputFiles) throws IOException { this.inputFiles = inputFiles; reset(); } public Sequence readNextSequence() throws IOException { if(currReader == null && !nextReader()) { return null; } Sequence ret; do { ret = currReader.readNextSequence(); } while(ret == null && nextReader()); return ret; } private boolean nextReader() throws IOException { close(); if(seqFileIndex >= inputFiles.size()) { return false; } currReader = new SequenceReader(inputFiles.get(seqFileIndex++)); return true; } public SequenceFormat getFormat() { if(currReader != null) { return currReader.getFormat(); } else { return SequenceFormat.UNKNOWN; } } public void close() throws IOException { if(currReader != null) { currReader.close(); currReader = null; } } public final void reset() throws IOException { close(); seqFileIndex = 0; nextReader(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/QSeqReader.java000066400000000000000000000112021247756524500244650ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.utils.SeqUtils; import java.io.File; import java.io.IOException; import java.util.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; /** * * @author fishjord */ public class QSeqReader implements SeqReader { private List seqids; private int seqIndex = 0; private IndexedSeqReader seqReader; private IndexedSeqReader qualReader = null; private SequenceFormat format; private boolean validate; public QSeqReader(File seqFile, File qualFile) throws IOException { this(seqFile, qualFile, true); } public QSeqReader(File seqFile, File qualFile, boolean validate) throws IOException { format = SeqUtils.guessFileFormat(seqFile); SequenceFormat qualFormat = SeqUtils.guessFileFormat(qualFile); if (format == SequenceFormat.FASTA && qualFormat == SequenceFormat.FASTA) { seqReader = new IndexedSeqReader(seqFile); qualReader = new IndexedSeqReader(qualFile, false, false); seqids = seqReader.getSeqIds(); if (validate) { Set qualIds = new HashSet(qualReader.getSeqIdSet()); Set tmpSeqIds = new HashSet(seqids); tmpSeqIds.removeAll(qualIds); qualIds.removeAll(seqids); if (!qualIds.isEmpty() || !tmpSeqIds.isEmpty()) { throw new IOException("Quality and sequence files don't contain the same sequences, non-matched qual-ids=" + qualIds + " non-matched seqids=" + tmpSeqIds); } } } else { throw new IOException("Both quality and sequence file must be in fasta format for reading from seperate files [sequence file format detected as " + format + " qual file format detected as " + qualFormat); } this.validate = validate; } public SequenceFormat getFormat() { return format; } public Sequence readNextSequence() throws IOException { if (seqIndex == seqids.size()) { return null; } return readSeq(seqids.get(seqIndex++)); } public List getSeqIds() { return Collections.unmodifiableList(seqids); } public byte[] readQual(String seqid) throws IOException { if(qualReader == null) { throw new IOException("No quality reader associated"); } Sequence qualSeq = qualReader.readSeq(seqid); String[] lexemes = qualSeq.getSeqString().trim().split("\\s+"); byte[] qual = new byte[lexemes.length]; for (int index = 0; index < lexemes.length; index++) { qual[index] = Byte.valueOf(lexemes[index]); } return qual; } public Sequence readPlainSequence(String seqid) throws IOException { return seqReader.readSeq(seqid); } public QSequence readSeq(String seqid) throws IOException { Sequence seq = seqReader.readSeq(seqid); byte[] qual = null; try { qual = readQual(seqid); } catch(IOException e) { if(validate) { throw e; } } if(validate) { int unalignedLength = SeqUtils.getUnalignedSeqString(seq.getSeqString()).length(); if (unalignedLength != qual.length) { throw new IOException("Sequence " + seq.getSeqName() + " length [" + seq.getSeqString().length() + "] doesn't equal quality sequence length [" + qual.length + "]"); } } else if(qual == null) { qual = new byte[SeqUtils.getUnalignedSeqString(seq.getSeqString()).length()]; } return new QSequence(seq, qual); } public void close() throws IOException { seqReader.close(); if (qualReader != null) { qualReader.close(); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/SeqReader.java000066400000000000000000000020311247756524500243440ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.SequenceFormat; import java.io.IOException; /** * * @author fishjord */ public interface SeqReader { public E readNextSequence() throws IOException; public SequenceFormat getFormat(); public void close() throws IOException; } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/Sequence.java000066400000000000000000000022151247756524500242450ustar00rootroot00000000000000/* * Sequence.java * * Copyright 2006 Michigan State University Board of Trustees * * Created on November 7, 2003, 5:41 PM */ package edu.msu.cme.rdp.readseq.readers; import java.io.Serializable; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; /** * An abstract class, providing an interface for accessing a sequence. * @author wangqion, fishjord */ public class Sequence implements Serializable { @XmlAttribute protected String seqName; @XmlAttribute protected String desc; @XmlElement protected String seqString; private Sequence() {} public Sequence(Sequence seq) { this(seq.seqName, seq.desc, seq.seqString); } public Sequence(String seqName, String desc, String seqString) { this.seqName = seqName; this.desc = desc; this.seqString = seqString; } public String getDesc() { return desc; } public String getSeqName() { return seqName; } public String getSeqString() { return seqString; } void setSeqString(String seqString) { this.seqString = seqString; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/SequenceReader.java000066400000000000000000000063521247756524500253760ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.readers.core.EMBLCore; import edu.msu.cme.rdp.readseq.readers.core.FastaCore; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.readers.core.GenbankCore; import edu.msu.cme.rdp.readseq.readers.core.SeqReaderCore; import edu.msu.cme.rdp.readseq.readers.core.SFFCore; import edu.msu.cme.rdp.readseq.readers.core.STKCore; import edu.msu.cme.rdp.readseq.readers.core.SeqReaderCore.EmptyCore; import edu.msu.cme.rdp.readseq.utils.SeqUtils; import java.io.BufferedInputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; import java.util.List; /** * * @author fishjord */ public class SequenceReader implements SeqReader { private SeqReaderCore core; private SequenceFormat format; public SequenceReader(File f) throws IOException { core = SeqUtils.getSeqReaderCore(f); format = SeqUtils.guessFileFormat(f); } public SequenceReader(InputStream in) throws IOException { core = SeqUtils.getSeqReaderCore(in); format = SequenceFormat.UNKNOWN; //XXX hack } public SequenceFormat getFormat() { return format; } public long getPosition() { return core.getPosition(); } public SequenceFormat getSeqFileFormat() { return format; } public Sequence readNextSequence() throws IOException { Sequence seq = core.readNextSequence(); if(seq != null) { seq.setSeqString(SeqUtils.filterSeqString(seq.getSeqString(), false)); } return seq; } public void close() throws IOException { core.close(); } public static List readFully(File f) throws IOException { SequenceReader reader = new SequenceReader(f); List ret = new ArrayList(); Sequence seq; try { while ((seq = reader.readNextSequence()) != null) { ret.add(seq); } return ret; } finally { reader.close(); } } public static List readFully(InputStream f) throws IOException { SequenceReader reader = new SequenceReader(f); List ret = new ArrayList(); Sequence seq; try { while ((seq = reader.readNextSequence()) != null) { ret.add(seq); } return ret; } finally { reader.close(); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/000077500000000000000000000000001247756524500225625ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/EMBLCore.java000066400000000000000000000152341247756524500247620ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.sequences.GenbankSequence; import java.io.DataOutputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.RandomAccessFile; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; import java.util.logging.Level; import java.util.logging.Logger; /** * * @author fishjord */ public class EMBLCore extends SeqReaderCore { public EMBLCore(File seqFile) throws IOException { super(seqFile); } public EMBLCore(InputStream is) throws IOException { super(is); } public Map scanInternal() throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); Map seqIndex = new LinkedHashMap(); while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); seqIndex.put(sid, lastHeader); readUntilNext("\n//"); lastHeader = seqFile.getFilePointer(); } seqFile.seek(firstHeader); return seqIndex; } public int scanToStream(DataOutputStream out) throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); Map seqIndex = new LinkedHashMap(); out.writeLong(seqFile.length()); out.writeUTF(SequenceFormat.EMBL.toString()); int written = 0; while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); out.writeUTF(sid); out.writeLong(lastHeader); written++; readUntilNext("\n//"); lastHeader = seqFile.getFilePointer(); } out.close(); seqFile.seek(firstHeader); return written; } @Override public Sequence readNextSeq() throws IOException { String line; String seqid = null, desc = "", seqString = null, organism = ""; Map> featureTable = new HashMap(); Map features = null; while ((line = readUntilNext('\n')) != null) { line = line.trim(); if (line.equals("//")) { break; } if (line.isEmpty()) { continue; } String[] lexemes = line.split("\\s+"); if (lexemes[0].equals("ID")) { seqid = lexemes[1].split(";")[0]; } else if (lexemes[0].equals("DE")) { if (!desc.isEmpty()) { desc += " "; } desc += line.substring(2).trim(); } else if (lexemes[0].equals("OS")) { if (!organism.isEmpty()) { organism += " "; } organism += line.substring(2).trim(); } else if (lexemes[0].equals("SQ")) { seqString = parseSeq(); break; //We assume SQ is the last entry in the record } else if (lexemes[0].equals("FT")) { if (lexemes[1].charAt(0) == '/') { String qual = line.substring(2).trim(); if (!qual.endsWith("\"") && qual.contains("\"")) { String rest = readUntilNext("\"\n"); for (String s : rest.split("\n")) { qual += s.substring(2).trim(); } } lexemes = qual.replace("\"", "").substring(1).split("="); if (lexemes.length != 2) { throw new IOException("Malformed qualifier " + qual + " in record " + seqid); } features.put(lexemes[0], lexemes[1]); } else if (lexemes.length == 3) { features = new HashMap(); features.put("location", lexemes[2]); featureTable.put(lexemes[1], features); } else { throw new IOException("Malformed qualifier " + line + " in record " + seqid); } } } if (seqid == null) { return null; } return new GenbankSequence(seqid, desc, organism, featureTable, seqString.replaceAll("\\s+", "")); } private String parseSid() throws IOException { return readUntilNext(' ', '\t', '\n', '\r'); } private String parseSeq() throws IOException { StringBuilder retSeq = new StringBuilder(); String seq = readUntilNext("//"); if (seq == null) { return null; } seq = seq.trim(); for (String line : seq.split("\n")) { line = line.trim(); if (line.isEmpty()) { continue; } int idx = line.lastIndexOf(" "); if (idx == -1) { Logger.getLogger(this.getClass().getCanonicalName()).log(Level.WARNING, "Weird sequence parsing seqbuffer={0}, currseq={1}", new Object[]{seq, retSeq}); continue; //Uhh, this is weird... } retSeq.append(line.substring(0, idx)); //We have to strip off the numbers... } return retSeq.toString(); } public static void main(String[] args) throws IOException { EMBLCore tmp = new EMBLCore(new File(args[0])); GenbankSequence seq = (GenbankSequence) tmp.readNextSeq(); System.out.println(seq.getSeqName()); System.out.println(seq.getDesc()); System.out.println(seq.getOrganism()); System.out.println(seq.getFeatureTable()); System.out.println(seq.getSeqString()); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/FastaCore.java000066400000000000000000000071641247756524500253040ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import java.io.DataOutputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.RandomAccessFile; import java.util.LinkedHashMap; import java.util.Map; /** * * @author fishjord */ public class FastaCore extends SeqReaderCore { public FastaCore(File seqFile) throws IOException { super(seqFile); readUntilNext('>'); } public FastaCore(InputStream is) throws IOException { super(is); readUntilNext('>'); } public Map scanInternal() throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); readUntilNext('>'); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); Map seqIndex = new LinkedHashMap(); while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); seqIndex.put(sid, lastHeader); readUntilNext("\n>"); lastHeader = seqFile.getFilePointer(); } seqFile.seek(firstHeader); return seqIndex; } public int scanToStream(DataOutputStream out) throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); readUntilNext('>'); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); Map seqIndex = new LinkedHashMap(); out.writeLong(seqFile.length()); out.writeUTF(SequenceFormat.FASTA.toString()); int written = 0; while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); out.writeUTF(sid); out.writeLong(lastHeader); written++; readUntilNext("\n>"); lastHeader = seqFile.getFilePointer(); } out.close(); seqFile.seek(firstHeader); return written; } @Override public Sequence readNextSeq() throws IOException { String header = parseHeader(); if (header == null) { return null; } String seq = parseSeq(); if (seq == null) { return null; } String seqid = header.split("\\s+")[0]; if (seqid.length() == header.length()) { header = ""; } else { header = header.substring(seqid.length()).trim(); } return new Sequence(seqid, header, seq.trim()); } private String parseSid() throws IOException { return readUntilNext(' ', '\t', '\n', '\r'); } private String parseHeader() throws IOException { return readUntilNext('\n'); } private String parseSeq() throws IOException { return readUntilNext("\n>"); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/FastqCore.java000066400000000000000000000126631247756524500253240ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import java.io.DataOutputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.RandomAccessFile; import java.util.LinkedHashMap; import java.util.Map; /** * * @author fishjord */ public class FastqCore extends SeqReaderCore { public static interface QualityFunction { public byte translate(char c); public char translate(byte b); } public static final QualityFunction Phred33QualFunction = new QualityFunction() { public byte translate(char c) { return (byte)(c - 33); } public char translate(byte q) { return (char)(((q <= 93) ? q : 93) + 33); } }; private QualityFunction qualFunction; public FastqCore(File seqFile) throws IOException { super(seqFile); readUntilNext('@'); this.qualFunction = Phred33QualFunction; } public FastqCore(InputStream seqFile) throws IOException { super(seqFile); readUntilNext('@'); this.qualFunction = Phred33QualFunction; } public Map scanInternal() throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); readUntilNext('@'); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); Map seqIndex = new LinkedHashMap(); while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); seqIndex.put(sid, lastHeader); String temp = readUntilNext("\n@"); // when @ is the first char of the quality line String[] lines = temp.split("\n"); if ( lines.length == 2){ readUntilNext("\n@"); } lastHeader = seqFile.getFilePointer(); } seqFile.seek(firstHeader); return seqIndex; } public int scanToStream(DataOutputStream out) throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); readUntilNext('@'); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); out.writeLong(seqFile.length()); out.writeUTF(SequenceFormat.FASTQ.toString()); int written = 0; while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); out.writeUTF(sid); out.writeLong(lastHeader); written++; readUntilNext("\n@"); lastHeader = seqFile.getFilePointer(); } out.close(); seqFile.seek(firstHeader); return written; } @Override public Sequence readNextSeq() throws IOException { String header = parseHeader(); if (header == null) { return null; } String seqid = header.split("\\s+")[0]; String seq = parseSeq(); if (seq == null) { return null; } String qualHeader = parseHeader(); if(qualHeader == null) { throw new IOException("Unexpected end of file when looking for qual seq for sequence " + seqid); } String qualId = qualHeader.split("\\s+")[0]; if(!qualId.equals(seqid) && !qualId.equals("")) { throw new IOException("Expected quality sequence for " + seqid + " but found quality sequence for " + qualId); } byte[] qual = parseQualSeq(); if(qual == null) { throw new IOException("Unexpected end of file when looking for qual seq for sequence " + seqid); } if (seqid.length() == header.length()) { header = ""; } else { header = header.substring(seqid.length()).trim(); } return new QSequence(seqid, header, seq.trim(), qual); } private String parseSid() throws IOException { return readUntilNext(' ', '\t', '\n', '\r'); } private String parseHeader() throws IOException { return readUntilNext('\n'); } private String parseSeq() throws IOException { String str = readSeqString("\n+"); return str; } private byte[] parseQualSeq() throws IOException { String str = readSeqString("\n@"); if(str == null) { return null; } byte[] ret = new byte[str.length()]; char[] seqChars = str.toCharArray(); for(int index = 0;index < seqChars.length;index++) { ret[index] = qualFunction.translate(seqChars[index]); } return ret; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/GenbankCore.java000066400000000000000000000111261247756524500256040ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import java.io.DataOutputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.RandomAccessFile; import java.util.LinkedHashMap; import java.util.Map; import java.util.logging.Level; import java.util.logging.Logger; /** * * @author fishjord */ public class GenbankCore extends SeqReaderCore { public GenbankCore(File seqFile) throws IOException { super(seqFile); } public GenbankCore(InputStream is) throws IOException { super(is); } public Map scanInternal() throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); Map seqIndex = new LinkedHashMap(); while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); seqIndex.put(sid, lastHeader); readUntilNext("\n//"); lastHeader = seqFile.getFilePointer(); } seqFile.seek(firstHeader); return seqIndex; } public int scanToStream(DataOutputStream out) throws IOException { RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(0); long firstHeader = seqFile.getFilePointer(); long lastHeader = seqFile.getFilePointer(); out.writeLong(seqFile.length()); out.writeUTF(SequenceFormat.GENBANK.toString()); int written = 0; while (seqFile.getFilePointer() != seqFile.length()) { String sid = parseSid(); out.writeUTF(sid); out.writeLong(lastHeader); written++; readUntilNext("\n//"); lastHeader = seqFile.getFilePointer(); } out.close(); seqFile.seek(firstHeader); return written; } @Override public Sequence readNextSeq() throws IOException { String line; String seqid = null, desc = "", seqString = null; while((line = readUntilNext('\n')) != null) { line = line.trim(); if(line.equals("//")) { break; } if(line.isEmpty()) { continue; } String[] lexemes = line.split("\\s+"); if(lexemes[0].equals("LOCUS")) { seqid = lexemes[1].split(";")[0]; } else if(lexemes[0].equals("DEFINITION")) { if(!desc.isEmpty()) { desc += " "; } desc += line.substring(2).trim(); } else if(lexemes[0].equals("ORIGIN")) { seqString = parseSeq(); break; //We assume ORIGIN is the last entry in the record } } if(seqid == null) { return null; } return new Sequence(seqid, desc, seqString.replaceAll("\\s+", "")); } private String parseSid() throws IOException { return readUntilNext(' ', '\t', '\n', '\r'); } private String parseSeq() throws IOException { StringBuilder retSeq = new StringBuilder(); String seq = readUntilNext("//"); if(seq == null) { return null; } seq = seq.trim(); for(String line : seq.split("\n")) { line = line.trim(); int idx = line.indexOf(" "); if(idx == -1) { Logger.getLogger(this.getClass().getCanonicalName()).log(Level.WARNING, "Weird sequence parsing seqbuffer={0}, currseq={1}", new Object[]{seq, retSeq}); continue; //Uhh, this is weird... } retSeq.append(line.substring(idx)); //We have to strip off the numbers... } return retSeq.toString(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/SFFCore.java000066400000000000000000000433741247756524500246670ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.utils.SeqUtils; import java.io.ByteArrayInputStream; import java.io.DataInput; import java.io.DataInputStream; import java.io.EOFException; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.RandomAccessFile; import java.util.ArrayList; import java.util.Arrays; import java.util.LinkedHashMap; import java.util.List; import org.apache.commons.lang.StringUtils; /** * * @author fishjord */ public class SFFCore extends SeqReaderCore { public static final int mftMagicNumber = 778921588; public static final int srtMagicNumber = 779317876; public static final int v1MagicNumber = 825110576; public static class CommonHeader { private int magicNumber; private int version; private long indexOffset; private int indexLength; private int numReads; private short headerLength; private short keyLength; private short flowLength; private byte flowgramFormat; private String flow; private String key; public String getFlow() { return flow; } public short getFlowLength() { return flowLength; } public byte getFlowgramFormat() { return flowgramFormat; } public short getHeaderLength() { return headerLength; } public int getIndexLength() { return indexLength; } public long getIndexOffset() { return indexOffset; } public String getKey() { return key; } public short getKeyLength() { return keyLength; } public int getMagicNumber() { return magicNumber; } public int getNumReads() { return numReads; } public int getVersion() { return version; } } public static class ReadBlock { private int headerLength; private int nameLength; private String name; private int numBases; private int clipQualLeft; private int clipQualRight; private int clipAdapterLeft; private int clipAdapterRight; private String seq; private short[] flowgrams; private byte[] flowIndex; private byte[] qual; public int getClipAdapterLeft() { return clipAdapterLeft; } public int getClipAdapterRight() { return clipAdapterRight; } public int getClipQualLeft() { return clipQualLeft; } public int getClipQualRight() { return clipQualRight; } public byte[] getFlowIndex() { return flowIndex; } public int getHeaderLength() { return headerLength; } public short[] getFlowgrams() { return flowgrams; } public String getName() { return name; } public int getNameLength() { return nameLength; } public int getNumBases() { return numBases; } public byte[] getQual() { return qual; } public String getSeq() { return seq; } } protected CommonHeader commonHeader; private String manifest; private static final int READ_BLOCK_STATIC_SIZE = 2 + 2 + 4 + 2 + 2 + 2 + 2; private static final int COMMON_HEADER_STATIC_SIZE = 4 + 4 + 8 + 4 + 4 + 2 + 2 + 2 + 1; public SFFCore(File f) throws IOException { super(f); parseCommonHeader(); } public SFFCore(InputStream is) throws IOException { super(is); parseCommonHeader(); } private void parseCommonHeader() throws IOException { if(commonHeader != null) { throw new IOException("Common header already initialized"); } commonHeader = new CommonHeader(); DataInput seqFile = super.getDataInput(); commonHeader.magicNumber = seqFile.readInt(); if (commonHeader.magicNumber != SeqUtils.SFF_MAGIC_NUMBER) { throw new IOException("Not an SFF File"); } commonHeader.version = seqFile.readInt(); if (commonHeader.version != 1) { throw new IOException("Cannot parse v" + commonHeader.version + " sff files"); } commonHeader.indexOffset = seqFile.readLong(); commonHeader.indexLength = seqFile.readInt(); commonHeader.numReads = seqFile.readInt(); commonHeader.headerLength = seqFile.readShort(); commonHeader.keyLength = seqFile.readShort(); commonHeader.flowLength = seqFile.readShort(); commonHeader.flowgramFormat = seqFile.readByte(); byte[] flow = new byte[commonHeader.flowLength]; super.read(flow); commonHeader.flow = new String(flow); byte[] key = new byte[commonHeader.keyLength]; super.read(key); commonHeader.key = new String(key); int readBytes = COMMON_HEADER_STATIC_SIZE + flow.length + key.length; alignToBoundary(readBytes); if (super.isSeekable() && commonHeader.indexOffset > commonHeader.headerLength) { readIndex(); } } public CommonHeader getCommonHeader() { return commonHeader; } public String getManifest() { return manifest; } @Override public LinkedHashMap scanInternal() throws IOException { if (commonHeader.indexOffset > commonHeader.headerLength) { return readIndex(); } RandomAccessFile seqFile = super.getRawFile(); seqFile.seek(commonHeader.headerLength); LinkedHashMap seqIndex = new LinkedHashMap(commonHeader.numReads); for (int index = 0; index < commonHeader.numReads; index++) { long pos = seqFile.getFilePointer(); ReadBlock block = readReadBlock(); seqIndex.put(block.name, pos); } return seqIndex; } @Override public QSequence readNextSeq() throws IOException { ReadBlock readBlock = readReadBlock(); if (readBlock == null) { return null; } int clipLeft = Math.max(readBlock.clipAdapterLeft, readBlock.clipQualLeft); int clipRight = readBlock.numBases; if (readBlock.clipAdapterRight > 0 && readBlock.clipAdapterRight < clipRight) { clipRight = readBlock.clipAdapterRight; } if (readBlock.clipQualRight != 0 && readBlock.clipQualRight < clipRight) { clipRight = readBlock.clipQualRight; } if (clipLeft > clipRight ) return readNextSeq(); String seq = readBlock.seq.substring(clipLeft - 1, clipRight); return new QSequence(readBlock.name, "", seq, Arrays.copyOfRange(readBlock.qual, clipLeft - 1, clipRight)); } public ReadBlock readReadBlock() throws IOException { try { DataInput seqFile = super.getDataInput(); ReadBlock ret = new ReadBlock(); /* * READ BLOCK HEADER */ ret.headerLength = seqFile.readShort(); ret.nameLength = seqFile.readShort(); int tmp = (ret.headerLength << 16) | ret.nameLength; if(tmp == mftMagicNumber) { //We ended up in the index...certainly possible return null; } ret.numBases = seqFile.readInt(); ret.clipQualLeft = seqFile.readUnsignedShort(); ret.clipQualRight = seqFile.readUnsignedShort(); ret.clipAdapterLeft = seqFile.readUnsignedShort(); ret.clipAdapterRight = seqFile.readUnsignedShort(); byte[] readName = new byte[ret.nameLength]; super.read(readName); int dataOffset = ret.headerLength - (ret.nameLength + READ_BLOCK_STATIC_SIZE); if (dataOffset < 0) { throw new IOException("Illegal ReadBlock header length (" + ret.headerLength + "), it would have me seek back in to the readblock"); } seqFile.skipBytes(dataOffset); /* * READ BLOCK DATA */ byte[] flowgramIndex = new byte[ret.numBases]; byte[] bases = new byte[ret.numBases]; byte[] quality = new byte[ret.numBases]; byte[] homopolymerStretchEstimates = new byte[(commonHeader.flowLength) * 2]; super.read(homopolymerStretchEstimates); super.read(flowgramIndex); super.read(bases); super.read(quality); DataInputStream flowgramStream = new DataInputStream(new ByteArrayInputStream(homopolymerStretchEstimates)); short[] flowgrams = new short[commonHeader.flowLength]; for (int index = 0; index < commonHeader.flowLength; index++) { flowgrams[index] = flowgramStream.readShort(); } flowgramStream.close(); ret.name = new String(readName); ret.flowgrams = flowgrams; ret.flowIndex = flowgramIndex; ret.seq = new String(bases); ret.qual = quality; int bytesRead = homopolymerStretchEstimates.length + flowgramIndex.length + bases.length + quality.length; alignToBoundary(bytesRead); return ret; } catch (EOFException e) { return null; } } private LinkedHashMap readIndex() throws IOException { if (commonHeader.indexOffset <= commonHeader.headerLength) { throw new IOException("Index offset is not set correctly"); } RandomAccessFile seqFile = super.getRawFile(); long seekBackTo = seqFile.getFilePointer(); seqFile.seek(commonHeader.indexOffset); long dataEnd = seqFile.getFilePointer(); LinkedHashMap seqIndex = new LinkedHashMap(commonHeader.numReads); int magicNumber = seqFile.readInt(); if (magicNumber == mftMagicNumber) { int version = seqFile.readInt(); if (version != v1MagicNumber) { throw new IOException("Can only parse .mft v1.0 indices"); } int xmlSize = seqFile.readInt(); int dataSize = seqFile.readInt(); dataEnd += dataSize; byte[] xml = new byte[xmlSize]; seqFile.read(xml); manifest = new String(xml); } else if (magicNumber == srtMagicNumber) { int version = seqFile.readInt(); if (version != v1MagicNumber) { throw new IOException("Can only parse .srt v1.0 indices"); } if (seqFile.read() != 0) { throw new IOException("Failed to find expected null byte in .srt header"); } dataEnd += commonHeader.indexLength; } else { throw new IOException("No supported index found"); } List currIndex = new ArrayList(); while (seqFile.getFilePointer() < dataEnd) { int b = seqFile.readUnsignedByte(); if (b == 0xff) { byte[] nameArray = new byte[currIndex.size() - 5]; long indexLoc = 0; int[] multipliers = new int[]{0, 16581375, 65025, 255, 1}; for (int i = 0; i < currIndex.size(); i++) { if (i < nameArray.length) { nameArray[i] = (byte) (currIndex.get(i) & 0xff); } else { int index = i - nameArray.length; indexLoc += currIndex.get(i) * multipliers[index]; } } String name = new String(nameArray); seqIndex.put(name, indexLoc); currIndex.clear(); } else { currIndex.add(b); } } seqFile.seek(seekBackTo); return seqIndex; } private void alignToBoundary(int bytesRead) throws IOException { int pos = bytesRead % 8; if (pos != 0) { pos = 8 - (pos % 8); } super.getDataInput().skipBytes(pos); } public static void main(String[] args) throws Exception { SFFCore core = new SFFCore(new File("test/454Reads.sff")); System.out.println("Common header:"); System.out.println(StringUtils.rightPad(" Version:", 20) + core.commonHeader.version); System.out.println(StringUtils.rightPad(" Index offset:", 20) + core.commonHeader.indexOffset); System.out.println(StringUtils.rightPad(" Index length:", 20) + core.commonHeader.indexLength); System.out.println(StringUtils.rightPad(" Num reads:", 20) + core.commonHeader.numReads); System.out.println(StringUtils.rightPad(" Header length:", 20) + core.commonHeader.headerLength); System.out.println(StringUtils.rightPad(" Key length:", 20) + core.commonHeader.keyLength); System.out.println(StringUtils.rightPad(" Num flows:", 20) + core.commonHeader.flowLength); System.out.println(StringUtils.rightPad(" Flowgram format:", 20) + core.commonHeader.flowgramFormat); System.out.println(StringUtils.rightPad(" Flow:", 20) + core.commonHeader.flow); System.out.println(StringUtils.rightPad(" Key:", 20) + core.commonHeader.key); System.out.println(); ReadBlock block = core.readReadBlock(); System.out.println(">" + block.name); System.out.println(StringUtils.rightPad(" Name:", 20) + block.name); System.out.println(StringUtils.rightPad(" Name length:", 20) + block.nameLength); System.out.println(StringUtils.rightPad(" Number of bases:", 20) + block.numBases); System.out.println(StringUtils.rightPad(" Length:", 20) + block.headerLength); System.out.println(StringUtils.rightPad(" Clip adapter left:", 20) + block.clipAdapterLeft); System.out.println(StringUtils.rightPad(" Clip adapter right:", 20) + block.clipAdapterRight); System.out.println(StringUtils.rightPad(" Clip qual left:", 20) + block.clipQualLeft); System.out.println(StringUtils.rightPad(" Clip qual right:", 20) + block.clipQualRight); System.out.print(StringUtils.rightPad("Flowgrams:", 20)); for (int index = 0; index < block.flowgrams.length; index++) { System.out.print(StringUtils.rightPad(block.flowgrams[index] + "", 10)); } System.out.println(); System.out.print(StringUtils.rightPad("Flow Indices:", 20)); for (int index = 0; index < block.flowIndex.length; index++) { System.out.print(StringUtils.rightPad(block.flowIndex[index] + "", 10)); } System.out.println(); System.out.print(StringUtils.rightPad("Sequence:", 20)); for (int index = 0; index < block.seq.length(); index++) { System.out.print(StringUtils.rightPad(block.seq.charAt(index) + "", 10)); } System.out.println(); System.out.print(StringUtils.rightPad("Quality:", 20)); for (int index = 0; index < block.qual.length; index++) { System.out.print(StringUtils.rightPad(block.qual[index] + "", 10)); } System.out.println(); System.out.println(); block = core.readReadBlock(); System.out.println(">" + block.name); System.out.println(StringUtils.rightPad(" Name:", 20) + block.name); System.out.println(StringUtils.rightPad(" Name length:", 20) + block.nameLength); System.out.println(StringUtils.rightPad(" Number of bases:", 20) + block.numBases); System.out.println(StringUtils.rightPad(" Length:", 20) + block.headerLength); System.out.println(StringUtils.rightPad(" Clip adapter left:", 20) + block.clipAdapterLeft); System.out.println(StringUtils.rightPad(" Clip adapter right:", 20) + block.clipAdapterRight); System.out.println(StringUtils.rightPad(" Clip qual left:", 20) + block.clipQualLeft); System.out.println(StringUtils.rightPad(" Clip qual right:", 20) + block.clipQualRight); System.out.print(StringUtils.rightPad("Flowgrams:", 20)); for (int index = 0; index < block.flowgrams.length; index++) { System.out.print(StringUtils.rightPad(block.flowgrams[index] + "", 10)); } System.out.println(); System.out.print(StringUtils.rightPad("Flow Indices:", 20)); for (int index = 0; index < block.flowIndex.length; index++) { System.out.print(StringUtils.rightPad(block.flowIndex[index] + "", 10)); } System.out.println(); System.out.print(StringUtils.rightPad("Sequence:", 20)); for (int index = 0; index < block.seq.length(); index++) { System.out.print(StringUtils.rightPad(block.seq.charAt(index) + "", 10)); } System.out.println(); System.out.print(StringUtils.rightPad("Quality:", 20)); for (int index = 0; index < block.qual.length; index++) { System.out.print(StringUtils.rightPad(block.qual[index] + "", 10)); } System.out.println(); core.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/STKCore.java000066400000000000000000000144641247756524500247100ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.io.File; import java.io.IOException; import java.io.RandomAccessFile; import java.util.ArrayList; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; /** * * @author fishjord */ public class STKCore extends SeqReaderCore { private Map> seqIndex = new LinkedHashMap(); private Map seqDescIndex = new LinkedHashMap(); private List seqids; public STKCore(File f) throws IOException { super(f); RandomAccessFile seqFile = super.getRawFile(); long firstSeqStart = -1; while (seqFile.getFilePointer() != seqFile.length()) { long currSeqIndex = seqFile.getFilePointer(); String lineStr = seqFile.readLine().trim(); char[] line = lineStr.toCharArray(); if (line.length == 0) { continue; //blank lines } else if (line.length == 2 && line[0] == '/' && line[1] == '/') { break; } String seqid; if (line[0] == '#') { if (line[1] != '=') { //comment continue; } if(line.length < 5) { throw new IOException("Malformed line " + lineStr); } char metaSeqType = line[3]; if (line[2] != 'G' || (metaSeqType != 'S' && metaSeqType != 'R' && metaSeqType != 'C')) { System.err.println("Unknown metasequence type " + lineStr.split("\\s+")[0] + ", not indexing"); continue; } if(line[4] != ' ') { throw new IOException("Malformed line " + lineStr); } StringBuilder sid = new StringBuilder(); for(int index = 5;index < line.length;index++) { if(line[index] == ' ') { break; } sid.append(line[index]); } if(metaSeqType == 'S') { //We're going to be bad and not process any sort of metaseqs besides GS and GC seqDescIndex.put(sid.toString(), currSeqIndex); continue; } else if(metaSeqType != 'C') { continue; } seqid = "#=GC " + sid.toString(); } else { StringBuilder sid = new StringBuilder(); for(int index = 0;index < line.length;index++) { if(line[index] == ' ') { break; } sid.append(line[index]); } seqid = sid.toString(); } if (firstSeqStart == -1) { firstSeqStart = currSeqIndex; } if (!seqIndex.containsKey(seqid)) { seqIndex.put(seqid, new ArrayList()); } seqIndex.get(seqid).add(currSeqIndex); } seqFile.seek(firstSeqStart); seqids = new ArrayList(seqIndex.keySet()); } @Override public LinkedHashMap scanInternal() throws IOException { LinkedHashMap ret = new LinkedHashMap(); for (String key : seqIndex.keySet()) { ret.put(key, seqIndex.get(key).get(0)); } return ret; } @Override public Sequence readNextSeq() throws IOException { RandomAccessFile seqFile = super.getRawFile(); long seqStart = seqFile.getFilePointer(); String line = seqFile.readLine().trim(); while (line.equals("")) { if (seqFile.getFilePointer() == seqFile.length()) { return null; } seqStart = seqFile.getFilePointer(); line = seqFile.readLine().trim(); } if (line.equals("//")) { return null; } String seqid = line.substring(0, line.lastIndexOf(" ")).trim(); if (seqIndex.get(seqid).get(0) != seqStart) { return null; } StringBuilder bases = new StringBuilder(); if (!seqIndex.containsKey(seqid)) { throw new IOException("Huh, that's odd, this sequence(" + seqid + ") didn't get indexed..."); } int nextSeqIndex = seqids.indexOf(seqid) + 1; long seekBackTo; if (nextSeqIndex == seqids.size()) { seekBackTo = seqFile.getFilePointer(); } else { seekBackTo = seqIndex.get(seqids.get(nextSeqIndex)).get(0); } for (long loc : seqIndex.get(seqid)) { seqFile.seek(loc); line = seqFile.readLine().trim(); bases.append(line.substring(line.lastIndexOf(" ") + 1).trim()); } String desc = ""; if (seqDescIndex.containsKey(seqid)) { seqFile.seek(seqDescIndex.get(seqid)); String[] lexemes = seqFile.readLine().split("\\s+"); if (!lexemes[0].equals("#=GS")) { throw new IOException("Sequence description index error!"); } if (!lexemes[1].equals(seqid)) { throw new IOException("I expected to find the description for " + seqid + " but I found the description for " + lexemes[1]); } for (int index = 3; index < lexemes.length; index++) { desc += lexemes[index] + " "; } desc = desc.trim(); } seqFile.seek(seekBackTo); return new Sequence(seqid, desc, bases.toString()); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/readers/core/SeqReaderCore.java000066400000000000000000000205501247756524500261130ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile; import java.io.BufferedInputStream; import java.io.DataInput; import java.io.DataInputStream; import java.io.EOFException; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.RandomAccessFile; import java.util.HashMap; import java.util.Map; /** * * @author fishjord */ public abstract class SeqReaderCore { public static class EmptyCore extends SeqReaderCore { public EmptyCore(File f) throws IOException { super(f); } public EmptyCore(InputStream is) throws IOException { super(is); } @Override public Map scanInternal() throws IOException { return new HashMap(); } @Override protected Sequence readNextSeq() throws IOException { return null; } } private boolean seekable; private RandomAccessFile rawRAFile = null; private DataInputStream is = null; public SeqReaderCore(File seqFile) throws IOException { this.rawRAFile = new BufferedRandomAccessFile(seqFile, "r", 4096); seekable = true; } public SeqReaderCore(InputStream is) throws IOException { this.is = new DataInputStream(new BufferedInputStream(is)); seekable = false; } protected final RandomAccessFile getRawFile() throws IOException { if (!seekable) { throw new IOException("Stream seq cores are not seekable"); } return rawRAFile; } protected final DataInput getDataInput() { if(seekable) { return rawRAFile; } else { return is; } } protected final int read(byte[] buf) throws IOException { if(seekable) { return rawRAFile.read(buf); } else { return is.read(buf); } } public boolean isSeekable() { return seekable; } /** * This function indexes the sequence file and returns to the start of the * first sequence when complete * @return * @throws IOException */ public Map scan() throws IOException { if (!seekable) { throw new IOException("This seq core is not seekable"); } return scanInternal(); } protected abstract Map scanInternal() throws IOException; /** * This function leaves off at the start of the next sequence * @param pos * @return * @throws IOException */ public Sequence parse(long pos) throws IOException { if (!seekable) { throw new IOException("This seq core is not seekable"); } rawRAFile.seek(pos); return readNextSeq(); } public void seek(long pos) throws IOException { if (!seekable) { throw new IOException("This seq core is not seekable"); } rawRAFile.seek(pos); } /** * This function should leave off at the start of the next sequence * @return * @throws IOException */ public Sequence readNextSequence() throws IOException { try { return this.readNextSeq(); } catch (EOFException e) { return null; } } protected abstract Sequence readNextSeq() throws IOException; public void close() throws IOException { if(seekable) { rawRAFile.close(); } else { is.close(); } } private int read() throws IOException { if(seekable) { return rawRAFile.read(); } else { return is.read(); } } public long getPosition() { if(!seekable) { return -1; } try { return rawRAFile.getFilePointer(); } catch (IOException e) { return -1; } } protected String readUntilNext(char... delims) throws IOException { StringBuilder ret = new StringBuilder(); int r, index; char c, prev = 0; while ((r = read()) != -1) { c = (char) r; if ((c == '\r' && prev == '\n') || (c == '\n' && prev == '\r')) { prev = c; continue; } prev = c; if (c == '\r') { c = '\n'; } prev = c; for (index = 0; index < delims.length; index++) { if (c == delims[index]) { return ret.toString(); } } ret.append(c); } if(ret.length() == 0) { return null; } return ret.toString(); } protected String readUntilNext(String delimStr) throws IOException { StringBuilder ret = new StringBuilder(); int checkIndex = 0, r; char c; char[] delim = delimStr.toCharArray(); char prev = 0; int i = 0; while ((r = read()) != -1) { c = (char) r; if ((c == '\r' && prev == '\n') || (c == '\n' && prev == '\r')) { prev = c; continue; } prev = c; if (c == '\r') { c = '\n'; } ret.append(c); if (c == delim[checkIndex]) { checkIndex++; if (checkIndex == delim.length) { return ret.substring(0, ret.length() - delim.length); } } else { if (delim[0] == c) { //Weird case where a first delim might be the character that fails the current delim check //Don't need to worry about checking the delim length cause if it was a match...we'd have returned when we first detected it checkIndex = 1; } else { checkIndex = 0; } } } if(ret.length() == 0) { return null; } return ret.toString(); } protected String readSeqString(String delimStr) throws IOException { StringBuilder ret = new StringBuilder(); int checkIndex = 0, r; char c; char[] delim = delimStr.toCharArray(); int delimLength = 0; for(int index = 0;index < delim.length;index++) { c = delim[index]; if(!(c == '\n' || c == ' ' || c == '\t')) { delimLength += 1; } } char prev = 0; int i = 0; while ((r = read()) != -1) { c = (char) r; if ((c == '\r' && prev == '\n') || (c == '\n' && prev == '\r')) { prev = c; continue; } prev = c; if (c == '\r') { c = '\n'; } if(!(c == '\n' || c == ' ' || c == '\t')) { ret.append(c); } if (c == delim[checkIndex]) { checkIndex++; if (checkIndex == delim.length) { return ret.substring(0, ret.length() - delimLength); } } else { if (delim[0] == c) { //Weird case where a first delim might be the character that fails the current delim check //Don't need to worry about checking the delim length cause if it was a match...we'd have returned when we first detected it checkIndex = 1; } else { checkIndex = 0; } } } if(ret.length() == 0) { return null; } return ret.toString(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/sequences/000077500000000000000000000000001247756524500222005ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/sequences/GenbankSequence.java000066400000000000000000000031461247756524500261050ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.sequences; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.util.Map; /** * * @author fishjord */ public class GenbankSequence extends Sequence { private Map> featureTable; private String organism; public GenbankSequence(String seqName, String desc, String organism, Map> featureTable, String seqString) { super(seqName, desc, seqString); this.organism = organism; this.featureTable = featureTable; } public GenbankSequence(Sequence seq, String organism, Map> featureTable) { super(seq); this.organism = organism; this.featureTable = featureTable; } public Map> getFeatureTable() { return featureTable; } public String getOrganism() { return organism; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/sequences/RDPSequence.java000066400000000000000000000024041247756524500251610ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.sequences; import edu.msu.cme.rdp.readseq.readers.Sequence; /** * * @author fishjord */ public class RDPSequence extends Sequence { private String internalId; public RDPSequence(String internalId, String seqName, String desc, String seqString) { super(seqName, desc, seqString); this.internalId = internalId; } public RDPSequence(Sequence seq, String internalId) { super(seq); this.internalId = internalId; } public String getInternalId() { return internalId; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/stat/000077500000000000000000000000001247756524500211605ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/stat/StdevCal.java000066400000000000000000000052141247756524500235320ustar00rootroot00000000000000package edu.msu.cme.rdp.readseq.stat; import java.util.ArrayList; import java.util.Collections; /** * * @author wangqion */ public class StdevCal { public static class Std{ private double totalCount; private double mean; private double stdev; Std(double t, double m, double s){ totalCount = t; mean = m; stdev = s; } public double getTotalCount(){ return totalCount; } public double getMean(){ return mean; } public double getStdev(){ return stdev; } } public static Std calStd(ArrayList valList){ double totalCount = 0.0; double valSum = 0; for ( Double d: valList){ if ( !d.isNaN()){ valSum += d.doubleValue(); totalCount++; } } double mean = valSum/totalCount; double sum = 0.0; for ( Double d: valList){ if ( !d.isNaN()){ sum += Math.pow(( d.doubleValue() - mean), 2); } } double stdev = Math.sqrt(sum/((double) totalCount -1)); Std stdResult = new Std(totalCount, mean, stdev); return stdResult; } public static double calMean(ArrayList valList){ double totalCount = 0.0; double valSum = 0; for ( Double d: valList){ if ( !d.isNaN()){ valSum += d.doubleValue(); totalCount++; } } if ( totalCount == 0){ return 0; }else { return valSum/totalCount; } } //calculate median public static double calMedian(ArrayList valList){ Collections.sort(valList); int middle = valList.size()/2; double medianValue = 0; //declare variable if (valList.size()%2 == 1) medianValue = valList.get(middle); else medianValue = (valList.get(middle-1) + valList.get(middle)) / 2; return medianValue; } public static void main(String[] args){ ArrayList valList = new ArrayList(); valList.add(5.0); valList.add(12.0); valList.add(16.0); valList.add(21.0); valList.add(14.0); valList.add(15.0); Std result = StdevCal.calStd(valList); System.out.println("totalCount= " + result.totalCount + " mean= " + result.mean + " std=" + result.stdev); System.out.println("mean " + StdevCal.calMean(valList)); System.out.println("median " + StdevCal.calMedian(valList)); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/000077500000000000000000000000001247756524500213455ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/AsciiUtils.java000066400000000000000000000046471247756524500242740ustar00rootroot00000000000000/* * * This program converts the accented characters to the their Ascii equivalent */ package edu.msu.cme.rdp.readseq.utils; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.io.InputStreamReader; import java.nio.charset.Charset; /** * * @author wangqion */ public class AsciiUtils { private static final String PLAIN_ASCII = "AaEeIiOoUu" // grave + "AaEeIiOoUuYy" // acute + "AaEeIiOoUuYy" // circumflex + "AaOoNn" // tilde + "AaEeIiOoUuYy" // umlaut + "Aa" // ring + "Cc" // cedilla + "OoUu" // double acute + "X" // x ; private static final String UNICODE = "\u00C0\u00E0\u00C8\u00E8\u00CC\u00EC\u00D2\u00F2\u00D9\u00F9" + "\u00C1\u00E1\u00C9\u00E9\u00CD\u00ED\u00D3\u00F3\u00DA\u00FA\u00DD\u00FD" + "\u00C2\u00E2\u00CA\u00EA\u00CE\u00EE\u00D4\u00F4\u00DB\u00FB\u0176\u0177" + "\u00C3\u00E3\u00D5\u00F5\u00D1\u00F1" + "\u00C4\u00E4\u00CB\u00EB\u00CF\u00EF\u00D6\u00F6\u00DC\u00FC\u0178\u00FF" + "\u00C5\u00E5" + "\u00C7\u00E7" + "\u0150\u0151\u0170\u0171" + "\u00D7" ; // private constructor, can't be instanciated! private AsciiUtils() { } // remove accentued from a string and replace with ascii equivalent public static String convertNonAscii(String s) { if (s == null) return null; StringBuilder sb = new StringBuilder(); int n = s.length(); for (int i = 0; i < n; i++) { char c = s.charAt(i); int pos = UNICODE.indexOf(c); if (pos > -1){ sb.append(PLAIN_ASCII.charAt(pos)); } else { sb.append(c); } } return sb.toString(); } public static void main(String args[]) throws IOException { String s = "The result : È,É,Ê,Ë,Û,Ù,Ï,Î,À,Â,Ã,Ô,è,é,ê,ë,û,ù,ï,î,à,â,ô,ç"; System.out.println(AsciiUtils.convertNonAscii(s)); // output : // The result : E,E,E,E,U,U,I,I,A,A,A,O,e,e,e,e,u,u,i,i,a,a,o,c BufferedReader taxreader = new BufferedReader(new InputStreamReader(new FileInputStream(new File(args[0])), Charset.forName("ISO-8859-1"))); String line; while ( (line = taxreader.readLine()) != null){ String newline = AsciiUtils.convertNonAscii(line); System.out.println(newline); } taxreader.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/BarcodeSorter.java000066400000000000000000000263141247756524500247540ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.utils.BarcodeUtils.BarcodeInvalidException; import edu.msu.cme.rdp.readseq.writers.FastqWriter; import edu.msu.cme.rdp.readseq.writers.SequenceWriter; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; /** * * @author fishjord */ public class BarcodeSorter { public static final String NoTag = "NoTag"; private static File getFastaFile(File workDir, String tag, String suffix) throws IOException { return new File(workDir, tag + suffix); } public static Map> sort(File seqFile, File tagFile) throws IOException, BarcodeInvalidException { return sortWithQual(seqFile, null, tagFile, new File(".")); } public static Map> sort(File seqFile, File tagFile, File workDir) throws IOException, BarcodeInvalidException { return sortWithQual(seqFile, null, tagFile, workDir); } public static Map> sortWithQual(File seqFile, File qualFile, File tagFile) throws IOException, BarcodeInvalidException { return sortWithQual(seqFile, qualFile, tagFile, new File(".")); } /** * Sorts the sequence file (and optional qual file) by barcodes * * This method will NOT complain if a sequence in the fasta file doesn't * have a qual file entry * * @param seqFile * @param qualFile * @param tagFile * @param workDir * @param makeDirForBarcode * @throws IOException * @throws * edu.msu.cme.rdp.readseq.utils.BarcodeUtils.BarcodeInvalidException */ public static Map> sortWithQual(File seqFile, File qualFile, File tagFile, File workDir) throws IOException, BarcodeInvalidException { SequenceFormat format = SeqUtils.guessFileFormat(seqFile); if (format != SequenceFormat.FASTA && qualFile != null && qualFile.exists()) { throw new IOException("Cannot provide an external quality file with non-fasta files"); } boolean hasQuality = (qualFile != null && qualFile.exists()) || format == SequenceFormat.FASTQ || format == SequenceFormat.SFF; Map> ret = new HashMap(); SequenceReader seqReader = new SequenceReader(seqFile); IndexedSeqReader qualReader = null; if (qualFile != null && qualFile.exists()) { qualReader = new IndexedSeqReader(qualFile, true, false); } Map tagToStream = new HashMap(); Map fileNameToStream = new HashMap(); Map barcodeMap = BarcodeUtils.readBarcodeFile(tagFile); barcodeMap.put(NoTag, NoTag); String tagName; for (String barcode : barcodeMap.keySet()) { File fileName = null; SequenceWriter stream = null; tagName = barcodeMap.get(barcode); if (hasQuality) { fileName = getFastaFile(workDir, tagName, ".fastq"); } else { fileName = getFastaFile(workDir, tagName, ".fasta"); } stream = fileNameToStream.get(fileName); if (stream == null) { if (!ret.keySet().contains(tagName)) { ret.put(tagName, new ArrayList()); } ret.get(tagName).add(fileName); if (hasQuality) { stream = new FastqWriter(fileName, FastqCore.Phred33QualFunction); } else { stream = new FastaWriter(fileName); } fileNameToStream.put(fileName, stream); } tagToStream.put(barcode, stream); } Sequence seq; while ((seq = readNextSequence(seqReader, qualReader)) != null) { boolean tagMatched = false; for (String barcode : tagToStream.keySet()) { if (seq.getSeqString().toLowerCase().indexOf(barcode) == 0) { tagToStream.get(barcode).writeSeq(seq); tagMatched = true; break; } } if (!tagMatched) { tagToStream.get(NoTag).writeSeq(seq); } } seqReader.close(); if (qualReader != null) { qualReader.close(); } for (String tag : tagToStream.keySet()) { tagToStream.get(tag).close(); } // check if file exists but is empty for (String barcode : barcodeMap.keySet()) { String tag = barcodeMap.get(barcode); File f = getFastaFile(workDir, tag, ".fasta"); File parent = f.getParentFile(); File q = getFastaFile(workDir, tag, ".fastq"); if (f.exists() && f.length() == 0) { f.delete(); //if delete seq file, delete the qual file if (q != null && q.exists() && q.length() == 0) { q.delete(); } } // delete the quality file if empty if (q != null && q.exists() && q.length() == 0) { q.delete(); } // delete the parent directory if empty if (parent.listFiles().length == 0) { parent.delete(); } } return ret; } /** * Sorts the sequence file (and optional qual file) by barcodes * * This method will NOT complain if a sequence in the fasta file doesn't * have a qual file entry * * @param seqFile * @param qualFile * @param tagFile * @param workDir * @param makeDirForBarcode * @throws IOException * @throws * edu.msu.cme.rdp.readseq.utils.BarcodeUtils.BarcodeInvalidException */ public static Map> sort(List seqFiles, File tagFile, File workDir, byte defaultQual) throws IOException, BarcodeInvalidException { SequenceFormat format; boolean hasQuality = false; for (File f : seqFiles) { format = SeqUtils.guessFileFormat(f); if (format == SequenceFormat.FASTQ || format == SequenceFormat.SFF) { hasQuality = true; break; } } Map> ret = new HashMap(); Map tagToStream = new HashMap(); Map fileNameToStream = new HashMap(); String tagName; File fileName; SequenceWriter stream; Map barcodeMap = BarcodeUtils.readBarcodeFile(tagFile); barcodeMap.put(NoTag, NoTag); for (String barcode : barcodeMap.keySet()) { tagName = barcodeMap.get(barcode); if (hasQuality) { fileName = getFastaFile(workDir, tagName, ".fastq"); } else { fileName = getFastaFile(workDir, tagName, ".fasta"); } stream = fileNameToStream.get(fileName); if (stream == null) { if (!ret.keySet().contains(tagName)) { ret.put(tagName, new ArrayList()); } ret.get(tagName).add(fileName); if (hasQuality) { stream = new FastqWriter(fileName, FastqCore.Phred33QualFunction, defaultQual); } else { stream = new FastaWriter(fileName); } fileNameToStream.put(fileName, stream); } tagToStream.put(barcode, stream); } SeqReader seqReader; Sequence seq; for (File seqFile : seqFiles) { seqReader = new SequenceReader(seqFile); while ((seq = seqReader.readNextSequence()) != null) { boolean tagMatched = false; for (String barcode : tagToStream.keySet()) { if (seq.getSeqString().toLowerCase().indexOf(barcode) == 0) { tagToStream.get(barcode).writeSeq(seq); tagMatched = true; break; } } if (!tagMatched) { tagToStream.get(NoTag).writeSeq(seq); } } seqReader.close(); } for (String tag : tagToStream.keySet()) { tagToStream.get(tag).close(); } for(String tag : ret.keySet()) { List files = ret.get(tag); Set remove = new HashSet(); for(File f : files) { if(f.exists() && f.length() == 0) { f.delete(); remove.add(f); } } files.removeAll(remove); } return ret; } private static Sequence readNextSequence(SequenceReader seqReader, IndexedSeqReader qualReader) throws IOException { Sequence ret = null; if (qualReader != null) { Sequence next = seqReader.readNextSequence(); if (next != null) { Sequence qualSeq = qualReader.readSeq(next.getSeqName()); String[] tokens = qualSeq.getSeqString().split("\\s+"); byte[] qual = new byte[tokens.length]; try { for (int index = 0; index < tokens.length; index++) { qual[index] = Byte.parseByte(tokens[index]); } } catch (NumberFormatException e) { throw new IOException("Invalid quality sequence for seq " + next.getSeqName()); } ret = new QSequence(next.getSeqName(), next.getDesc(), next.getSeqString(), qual); } } else { ret = seqReader.readNextSequence(); } return ret; } public static void main(String[] args) throws Exception { //BarcodeSorter.sort(new File(args[0]), new File(args[1]), new File(args[2])); BarcodeSorter.sortWithQual(new File(args[0]), new File(args[1]), new File(args[2]), new File(args[3])); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/BarcodeUtils.java000066400000000000000000000072451247756524500246000ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.Reader; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; /** * * @author fishjord */ public class BarcodeUtils { public static class BarcodeInvalidException extends Exception { public BarcodeInvalidException(String str) { super(str); } } public static Map readBarcodeFile(File barcodeFile) throws IOException, BarcodeInvalidException { return readBarcodeFile(new FileReader(barcodeFile)); } public static Map readBarcodeFile(InputStream is) throws IOException, BarcodeInvalidException { return readBarcodeFile(new InputStreamReader(is)); } /** * Reads a barcode (tag file) and returns a map of barcodes to sample names * * @param barcodeFile barcode fiel to read * @return map of barcodes to sample names * @throws IOException * @throws edu.msu.cme.rdp.readseq.utils.BarcodeUtils.BarcodeInvalidException if there are duplicate barcodes or a barcode is a prefix to another */ public static Map readBarcodeFile(Reader r) throws IOException, BarcodeInvalidException { Map ret = new HashMap(); BufferedReader reader = null; if (reader instanceof BufferedReader) { reader = (BufferedReader) r; } else { reader = new BufferedReader(r); } String line; while ((line = reader.readLine()) != null) { String[] tokens = line.trim().split("\\s+"); if (tokens.length != 2 && tokens.length != 3) { continue; } String tag = tokens[0].toLowerCase(); if (ret.containsKey(tag)) { throw new BarcodeInvalidException("Barcode for " + ret.get(tag) + " and " + tokens[1] + " are both " + tag); } ret.put(tag, tokens[1]); } reader.close(); List barcodes = new ArrayList(ret.keySet()); for (int row = 0; row < barcodes.size(); row++) { String barcode1 = barcodes.get(row); for (int col = row + 1; col < barcodes.size(); col++) { String barcode2 = barcodes.get(col); if (barcode1.startsWith(barcode2)) { throw new BarcodeInvalidException("Barcode " + barcode2 + " (" + ret.get(barcode2) + ") is a prefix of barcode " + barcode1 + " (" + ret.get(barcode1) + ")"); } if (barcode2.startsWith(barcode1)) { throw new BarcodeInvalidException("Barcode " + barcode1 + " (" + ret.get(barcode1) + ") is a prefix of barcode " + barcode2 + " (" + ret.get(barcode2) + ")"); } } } return ret; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/BufferedRandomAccessFile.java000066400000000000000000000113731247756524500270220ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import java.io.File; import java.io.IOException; import java.io.RandomAccessFile; /** * * @author fishjord */ public class BufferedRandomAccessFile extends RandomAccessFile { private byte[] buf; private long realPos; private int bufPos; private int bufEnd; private boolean sync = false; public BufferedRandomAccessFile(File f, String mode, int bufSize) throws IOException { super(f, mode); buf = new byte[bufSize]; fillBuffer(); } @Override public int skipBytes(int n) throws IOException{ return super.skipBytes(n); } @Override public final int read() throws IOException { if (bufPos >= bufEnd) { if (fillBuffer() < 0) { return -1; } } if (bufEnd == 0) { return -1; } else { return buf[bufPos++] & 0xff; } } @Override public int read(byte b[]) throws IOException { return read(b, 0, b.length); } @Override public int read(byte b[], int off, int len) throws IOException { int readCount = 0; for(int index = off;index < len;index++) { int r = this.read(); if(r == -1) { break; } readCount++; b[index] = (byte)r; } return readCount; } @Override public final void write(int b) throws IOException { if (bufPos >= buf.length) { fillBuffer(); } buf[bufPos++] = (byte) b; if (bufPos >= bufEnd) { bufEnd = bufPos; } sync = true; } @Override public long getFilePointer() throws IOException { long l = realPos; return (l - bufEnd + bufPos); } @Override public void seek(long pos) throws IOException { int n = (int) (realPos - pos); if (n >= 0 && n <= bufEnd) { bufPos = bufEnd - n; } else { sync(); super.seek(pos); invalidate(); } } @Override public void write(byte[] b) throws IOException { throw new UnsupportedOperationException(); } @Override public void write(byte b[], int off, int len) throws IOException { throw new UnsupportedOperationException(); } @Override public void close() throws IOException { sync(); super.close(); } private void sync() throws IOException { if (sync) { super.seek(realPos - bufEnd); super.write(buf, 0, bufEnd); sync = false; //invalidate(); } } private int fillBuffer() throws IOException { sync(); int n = super.read(buf, 0, buf.length); if (n >= 0) { //System.out.println("Filling buffer...read in " + n + " bytes"); realPos += n; bufEnd = n; bufPos = 0; } return n; } private void invalidate() throws IOException { bufEnd = 0; bufPos = 0; realPos = super.getFilePointer(); } public static void main(String[] args) throws Exception { try { File file = new File("tmp.bin"); if (file.exists()) { file.delete(); } BufferedRandomAccessFile f = new BufferedRandomAccessFile(file, "rw", 1); f.writeInt(1); f.writeInt(2); f.writeInt(3); f.writeInt(4); f.writeInt(5); f.seek(0); System.out.println(f.readInt()); System.out.println(f.readInt()); f.writeInt(6); System.out.println(f.readInt()); System.out.println(f.readInt()); f.seek(0); System.out.println(f.readInt()); System.out.println(f.readInt()); System.out.println(f.readInt()); System.out.println(f.readInt()); System.out.println(f.readInt()); f.close(); } catch (Exception e) { } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/IUBUtilities.java000066400000000000000000000270141247756524500245270ustar00rootroot00000000000000/* * Copyright (C) 2012 Michigan State University * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; public class IUBUtilities { public static boolean isIUB(char base) { switch (base) { case '~': case '.': case '-': case 'A': case 'a': case 'C': case 'c': case 'G': case 'g': case 'U': case 'u': case 'T': case 't': case 'N': case 'n': case 'X': case 'x': case 'M': case 'm': case 'R': case 'r': case 'W': case 'w': case 'S': case 's': case 'Y': case 'y': case 'K': case 'k': case 'V': case 'v': case 'H': case 'h': case 'D': case 'd': case 'B': case 'b': case 'I': case 'i': return true; default: return false; } } public static boolean isIUB(byte[] bases) { for (int i = 0; i < bases.length; i++) { if (isIUB((char) bases[i]) == false) { return false; } } return true; } public static boolean isIUB(char[] bases) { for (int i = 0; i < bases.length; i++) { if (isIUB(bases[i]) == false) { return false; } } return true; } public static boolean isGap(char base) { switch (base) { case '~': case '.': case '-': return true; default: return false; } } public static boolean isAmbiguity(char base) { switch (base) { case 'N': case 'n': case 'X': case 'x': case 'M': case 'm': case 'R': case 'r': case 'W': case 'w': case 'S': case 's': case 'Y': case 'y': case 'K': case 'k': case 'V': case 'v': case 'H': case 'h': case 'D': case 'd': case 'I': case 'i': case 'B': case 'b': return true; default: return false; } } public static boolean isACGU(char base) { switch (base) { case 'A': case 'a': case 'C': case 'c': case 'G': case 'g': case 'U': case 'u': case 'T': case 't': return true; default: return false; } } /** * IUPAC nucleotide bases * @param base * @return */ public static boolean isIUPACDNA(char base) { switch (base) { case 'A': case 'a': case 'C': case 'c': case 'G': case 'g': case 'U': case 'u': case 'T': case 't': case 'N': case 'n': case 'M': case 'm': case 'R': case 'r': case 'W': case 'w': case 'S': case 's': case 'Y': case 'y': case 'K': case 'k': case 'V': case 'v': case 'H': case 'h': case 'D': case 'd': case 'B': case 'b': return true; default: return false; } } public static boolean isA(char base) { switch (base) { case 'A': case 'a': case 'R': case 'r': case 'M': case 'm': case 'W': case 'w': case 'H': case 'h': case 'V': case 'v': case 'D': case 'd': case 'I': case 'i': case 'N': case 'n': return true; default: return false; } } public static boolean isC(char base) { switch (base) { case 'C': case 'c': case 'Y': case 'y': case 'M': case 'm': case 'S': case 's': case 'H': case 'h': case 'B': case 'b': case 'V': case 'v': case 'N': case 'n': return true; default: return false; } } public static boolean isG(char base) { switch (base) { case 'G': case 'g': case 'R': case 'r': case 'K': case 'k': case 'S': case 's': case 'B': case 'b': case 'V': case 'v': case 'D': case 'd': case 'I': case 'i': case 'N': case 'n': return true; default: return false; } } public static boolean isU(char base) { switch (base) { case 'U': case 'u': case 'T': case 't': case 'Y': case 'y': case 'K': case 'k': case 'W': case 'w': case 'H': case 'h': case 'B': case 'b': case 'D': case 'd': case 'I': case 'i': case 'N': case 'n': return true; default: return false; } } public static boolean matches(char b1, char b2) { return (isA(b1) && isA(b2)) || (isC(b1) && isC(b2)) || (isG(b1) && isG(b2)) || (isU(b1) && isU(b2)); } public static String makeProper(String seq) { StringBuffer properSeq = new StringBuffer(""); for (int i = 0; i < seq.length(); i++) { switch (seq.charAt(i)) { case '~': case '.': case '-': properSeq = properSeq.append("-"); break; case 'A': case 'a': properSeq = properSeq.append("A"); break; case 'C': case 'c': properSeq = properSeq.append("C"); break; case 'G': case 'g': properSeq = properSeq.append("G"); break; case 'U': case 'u': case 'T': case 't': properSeq = properSeq.append("T"); break; case 'N': case 'n': properSeq = properSeq.append("N"); break; case 'X': case 'x': properSeq = properSeq.append("X"); break; case 'M': case 'm': properSeq = properSeq.append("M"); break; case 'R': case 'r': properSeq = properSeq.append("R"); break; case 'W': case 'w': properSeq = properSeq.append("W"); break; case 'S': case 's': properSeq = properSeq.append("S"); break; case 'Y': case 'y': properSeq = properSeq.append("Y"); break; case 'K': case 'k': properSeq = properSeq.append("K"); break; case 'V': case 'v': properSeq = properSeq.append("V"); break; case 'H': case 'h': properSeq = properSeq.append("H"); break; case 'D': case 'd': properSeq = properSeq.append("D"); break; case 'I': case 'i': properSeq = properSeq.append("D"); break; case 'B': case 'b': properSeq = properSeq.append("B"); break; default: break; } } return properSeq.toString(); } public static String reverseComplement(String bases) { return reverse(complement(bases)); } public static char[] reverseComplement(char[] bases) { return reverse(complement(bases)); } public static String reverse(String str) { return new String(reverse(str.toCharArray())); } public static char[] reverse(char[] bases) { char[] ret = new char[bases.length]; for(int i = bases.length;i > 0;i--) { ret[bases.length - i] = bases[i - 1]; } return ret; } public static String complement(String bases) { return new String(complement(bases.toCharArray())); } public static char[] complement(char[] bases) { char[] ret = new char[bases.length]; for (int index = 0; index < bases.length; index++) { switch (bases[index]) { case '~': case '.': case '-': ret[index] = '-'; break; case 'A': case 'a': ret[index] = 'T'; break; case 'C': case 'c': ret[index] = 'G'; break; case 'G': case 'g': ret[index] = 'C'; break; case 'U': case 'u': case 'T': case 't': ret[index] = 'A'; break; case 'N': case 'n': ret[index] = 'N'; break; case 'X': case 'x': ret[index] = 'X'; break; case 'M': case 'm': ret[index] = 'K'; break; case 'R': case 'r': ret[index] = 'Y'; break; case 'W': case 'w': ret[index] = 'W'; break; case 'S': case 's': ret[index] = 'S'; break; case 'Y': case 'y': ret[index] = 'R'; break; case 'K': case 'k': ret[index] = 'M'; break; case 'V': case 'v': ret[index] = 'B'; break; case 'H': case 'h': ret[index] = 'D'; break; case 'D': case 'd': ret[index] = 'H'; break; case 'I': case 'i': ret[index] = 'H'; break; case 'B': case 'b': ret[index] = 'V'; break; default: break; } } return ret; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/NuclBinMapping.java000066400000000000000000000060371247756524500250640ustar00rootroot00000000000000/* * Copyright (C) 2013 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import java.util.Arrays; /** * * @author Jordan Fish */ public class NuclBinMapping { public static final char[] intToChar = new char[]{'a', 'c', 'g', 't'}; public static final byte[] validateLookup = new byte[127]; public static final byte[] complementLookup = new byte[127]; public static final int a = 0; public static final int c = 1; public static final int g = 2; public static final int t = 3; static { Arrays.fill(validateLookup, (byte) -1); validateLookup['A'] = a; validateLookup['C'] = c; validateLookup['G'] = g; validateLookup['T'] = t; validateLookup['a'] = a; validateLookup['c'] = c; validateLookup['g'] = g; validateLookup['t'] = t; validateLookup['U'] = t; validateLookup['u'] = t; Arrays.fill(complementLookup, (byte) -1); complementLookup['A'] = t; // A complementLookup['T'] = a; // T complementLookup['U'] = a; // U complementLookup['G'] = c; // G complementLookup['C'] = g; // C complementLookup['a'] = t; // a complementLookup['t'] = a; // t complementLookup['u'] = a; // t complementLookup['g'] = c; // g complementLookup['c'] = g; // c complementLookup[a] = t; // a complementLookup[t] = a; // t complementLookup[g] = c; // g complementLookup[c] = g; // c } public static String fromByteArray(byte[] seq) { StringBuilder ret = new StringBuilder(); for(byte b : seq) { if(b > intToChar.length) { throw new IllegalArgumentException("Bases are expected to be in the range [0-3]"); } else { ret.append(intToChar[b]); } } return ret.toString(); } public static byte[] toBytes(String seq) { char[] bases = seq.toCharArray(); byte[] ret = new byte[bases.length]; byte b; for(int index = 0;index < bases.length;index++) { b = validateLookup[bases[index]]; if(b == -1) { throw new IllegalArgumentException("Unable to process base " + (index + 1) + " (" + bases[index] + ")"); } ret[index] = b; } return ret; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/ProtBinMapping.java000066400000000000000000000027451247756524500251110ustar00rootroot00000000000000/* * Copyright (C) 2014 wangqion * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import java.util.Arrays; /** * * @author wangqion */ public class ProtBinMapping { public static final byte[] asciiMap = new byte[127]; public static final char[] intToChar = new char[127]; static { byte alpha = 0; Arrays.fill(asciiMap, (byte) -1); for (char c : SeqUtils.proteinAlphabet) { if (Character.isUpperCase(c)) { asciiMap[c] = asciiMap[Character.toLowerCase(c)] = alpha; intToChar[alpha] = Character.toLowerCase(c); alpha++; } } intToChar[alpha] = '*'; asciiMap['*'] = alpha++; if (alpha != 26) { throw new IllegalStateException("More than 25 amino acids..."); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/ProteinUtils.java000077500000000000000000000334201247756524500246560ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.utils.gbregion.Extends; import edu.msu.cme.rdp.readseq.utils.gbregion.SingleSeqRegion; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Set; import java.util.regex.Matcher; import java.util.regex.Pattern; /** * * @author fishjord */ public class ProteinUtils { public static final char UNKNOWN_AA = 'X'; public static class AminoAcid { private Character aminoAcid; private boolean initiator; public AminoAcid(Character aminoAcid, boolean initiator) { this.aminoAcid = Character.toLowerCase(aminoAcid); this.initiator = initiator; } public Character getAminoAcid() { return aminoAcid; } public boolean isInitiator() { return initiator; } public boolean matches(char c) { return aminoAcid == Character.toLowerCase(c); } } private Map translationTableMap = new LinkedHashMap(); private static final Pattern tableIdPattern = Pattern.compile("transl_table=(\\d+)"); private static final Pattern tableEntryPattern = Pattern.compile("([A-Z]{3})\\s+([A-Z*]{1})\\s+[A-Z][a-z]{2}(\\s+i)?"); private static final byte[] asciiMap = new byte[127]; static { Arrays.fill(asciiMap, (byte)-1); asciiMap['A'] = asciiMap['a'] = 0; asciiMap['C'] = asciiMap['c'] = 1; asciiMap['G'] = asciiMap['g'] = 2; asciiMap['T'] = asciiMap['t'] = asciiMap['U'] = asciiMap['u'] = 3; } private static class ProteinUtilsHolder { private static ProteinUtils holder = new ProteinUtils(); } private static class TranslateResult { int errors; String translStr; } private ProteinUtils() { try { BufferedReader reader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream("/data/protein_coding_tables.txt"))); String line; Integer currTable = -1; AminoAcid[][][] translationTable = new AminoAcid[4][4][4]; while ((line = reader.readLine()) != null) { Matcher m = tableIdPattern.matcher(line); if (m.find()) { if (currTable != -1) { translationTableMap.put(currTable, translationTable); } currTable = new Integer(m.group(1)); translationTable = new AminoAcid[4][4][4]; } else { m = tableEntryPattern.matcher(line); while (m.find()) { String strCodon = m.group(1).toLowerCase(); AminoAcid aa = new AminoAcid(m.group(2).charAt(0), m.group().endsWith("i")); Set codons = new HashSet(); codons.add(strCodon.toLowerCase()); if (strCodon.contains("t")) { codons.add(strCodon.replace("t", "u")); } if (strCodon.contains("u")) { codons.add(strCodon.replace("u", "t")); } for (String c : codons) { char[] codon = strCodon.toCharArray(); if (codon.length != 3) { throw new IOException("Unexpected codon length in line " + line); } translationTable[asciiMap[codon[0]]][asciiMap[codon[1]]][asciiMap[codon[2]]] = aa; } } } } if (!translationTableMap.containsKey(currTable)) { translationTableMap.put(currTable, translationTable); } } catch (IOException e) { throw new RuntimeException(e); } } public AminoAcid[][][] getTranslationTable(int table) { return translationTableMap.get(table); } public int proteinTables() { return translationTableMap.size(); } public static ProteinUtils getInstance() { return ProteinUtilsHolder.holder; } public String translateToProtein(String unalignedNucSeq, boolean dontAllowInitiators, int translTable) { AminoAcid[][][] proteinMapping = translationTableMap.get(translTable); if (proteinMapping == null) { throw new IllegalArgumentException("No such protein translation table " + translTable); } StringBuilder ret = new StringBuilder(); char[] bases = unalignedNucSeq.toLowerCase().toCharArray(); for (int index = 0; index + 3 <= bases.length; index += 3) { AminoAcid aa = null; if(asciiMap[bases[index]] != -1 && asciiMap[bases[index + 1]] != -1 && asciiMap[bases[index + 2]] != -1) { aa = proteinMapping[asciiMap[bases[index]]][asciiMap[bases[index + 1]]][asciiMap[bases[index + 2]]]; } if (aa == null) { ret.append(UNKNOWN_AA); } else { if (index == 0 && !dontAllowInitiators && aa.isInitiator()) { ret.append('m'); } else { ret.append(aa.getAminoAcid()); } } } return ret.toString(); } private TranslateResult backTranslate(String protSeq, String unalignedNucSeq, boolean dontAllowInitiators, int translTable) { AminoAcid[][][] proteinMapping = translationTableMap.get(translTable); if (proteinMapping == null) { throw new IllegalArgumentException("No such protein translation table " + translTable); } int unalignedIndex = 0; int errors = 0; char[] bases = unalignedNucSeq.toLowerCase().toCharArray(); StringBuilder nucSeq = new StringBuilder(); for (int index = 0; index < protSeq.length(); index++) { char protBase = protSeq.charAt(index); int nucSeqIndex = unalignedIndex * 3; if (protBase == 'x' || protBase == 'X') { // if the aa is "X", do not check if the nucleotide bases match the aa base nucSeq.append(Character.toLowerCase(bases[nucSeqIndex])).append(Character.toLowerCase(bases[nucSeqIndex + 1])).append(Character.toLowerCase(bases[nucSeqIndex + 2])); unalignedIndex ++; }else if (Character.isLetter(protBase)) { if (nucSeqIndex + 3 > unalignedNucSeq.length() + 1) { throw new IllegalStateException("Ran out of nucleotides but there were still proteins..."); } char p = protBase; AminoAcid aa = null; if(asciiMap[bases[nucSeqIndex]] != -1 && asciiMap[bases[nucSeqIndex + 1]] != -1 && asciiMap[bases[nucSeqIndex + 2]] != -1) { aa = proteinMapping[asciiMap[bases[nucSeqIndex]]][asciiMap[bases[nucSeqIndex + 1]]][asciiMap[bases[nucSeqIndex + 2]]]; } if (aa != null) { char aminoAcid = aa.getAminoAcid(); if (index == 0 && !dontAllowInitiators && aa.isInitiator()) { aminoAcid = 'm'; } if (Character.toUpperCase(aminoAcid) != Character.toUpperCase(p)) { errors++; } } else { throw new IllegalArgumentException("Failed to translate codon: " + bases[nucSeqIndex] + "" + bases[nucSeqIndex + 1] + "" + bases[nucSeqIndex + 2]); } if (Character.isUpperCase(protBase)) { nucSeq.append(Character.toUpperCase(bases[nucSeqIndex])).append(Character.toUpperCase(bases[nucSeqIndex + 1])).append(Character.toUpperCase(bases[nucSeqIndex + 2])); } else { nucSeq.append(Character.toLowerCase(bases[nucSeqIndex])).append(Character.toLowerCase(bases[nucSeqIndex + 1])).append(Character.toLowerCase(bases[nucSeqIndex + 2])); } unalignedIndex++; } else if (protBase == '-') { nucSeq.append("---"); } else if (protBase == '.') { nucSeq.append("..."); } else if(protBase == '*') { //So we're going to go ahead and not choke on a stop codon //This has several implications, first if we see a * we can't tell if it is suppose //to be a model or non-model position based only on the sequence string. Thankfully //for now HMMER3 will push *s to inserts, so we should be able to safely insert the //codon in lower case if (index + 1 != protSeq.length()) { //If this is a stop codon not at the end...that's a problem errors++; } unalignedIndex++; nucSeq.append(Character.toLowerCase(bases[nucSeqIndex])).append(Character.toLowerCase(bases[nucSeqIndex + 1])).append(Character.toLowerCase(bases[nucSeqIndex + 2])); } else { throw new IllegalArgumentException("Unexpected amino acid '" + protBase + "'"); } } TranslateResult result = new TranslateResult(); result.errors = errors; result.translStr = nucSeq.toString(); return result; } public String getAlignedNucSeq(String alignedProtSeq, String unalignedNucSeq, SingleSeqRegion r, int translTable) { return backTranslate(alignedProtSeq, unalignedNucSeq, (r.getExtends() == Extends.BEYOND_BEGIN || r.getExtends() == Extends.BEYOND_BOTH), translTable).translStr; } public float getTranslScore(String proteinSeq, String nucSeq, SingleSeqRegion r, int translTable) { int errors = backTranslate(proteinSeq, nucSeq, (r.getExtends() == Extends.BEYOND_BEGIN || r.getExtends() == Extends.BEYOND_BOTH), translTable).errors; return ((proteinSeq.length() - errors) / (float) proteinSeq.length()); } public String getAlignedNucSeq(String alignedProtSeq, String unalignedNucSeq, boolean dontAllowInitiators, int translTable) { return backTranslate(alignedProtSeq, unalignedNucSeq, dontAllowInitiators, translTable).translStr; } public float getTranslScore(String proteinSeq, String nucSeq, boolean dontAllowInitiators, int translTable) { int errors = backTranslate(proteinSeq, nucSeq, dontAllowInitiators, translTable).errors; return ((proteinSeq.length() - errors) / (float) proteinSeq.length()); } public List allTranslate(Sequence seq) { String seqString = seq.getSeqString(); List ret = new ArrayList(); if (seqString.length() < 3) { return ret; } for (int frame = 0; frame < 3; frame++) { String frameSeq = seqString.substring(frame); String reverseFrameSeq = IUBUtilities.reverseComplement(seqString).substring(frame); if (frameSeq.length() < 3) { continue; } ret.add(new Sequence(seq.getSeqName() + "_" + (frame + 1), "", translateToProtein(frameSeq, true, 11))); ret.add(new Sequence(seq.getSeqName() + "_-" + (frame + 1), "", translateToProtein(reverseFrameSeq, true, 11))); } return ret; } public List allFrames(Sequence seq) { String seqString = seq.getSeqString(); List ret = new ArrayList(); if (seqString.length() < 3) { return ret; } for (int frame = 0; frame < 3; frame++) { String frameSeq = seqString.substring(frame); String reverseFrameSeq = IUBUtilities.reverseComplement(seqString).substring(frame); if (frameSeq.length() < 3) { continue; } ret.add(new Sequence(seq.getSeqName() + "_" + (frame + 1), "", frameSeq)); ret.add(new Sequence(seq.getSeqName() + "_-" + (frame + 1), "", reverseFrameSeq)); } return ret; } public static void main(String[] args) { Map codonToProt = new HashMap(); int i = 0; for(String s : "A C D E F G H I K L M N P Q R S T V W Y".split("\\s+")) { codonToProt.put(s.charAt(0), i); System.out.println(s + " " + i); i++; } codonToProt.put('*', -1); char[] nucl = new char[]{'a', 'c', 'g', 't'}; for(char b1 : nucl) { for(char b2 : nucl) { for(char b3 : nucl) { Character aa = Character.toUpperCase(ProteinUtils.getInstance().translationTableMap.get(11)[asciiMap[b1]][asciiMap[b2]][asciiMap[b3]].getAminoAcid()); System.out.println("bct_codons[twobit_repr('" + b1 + "') << 4 | twobit_repr('" + b2 + "') << 2 | twobit_repr('" + b3 + "')] = " + codonToProt.get(aa) + "; //" + aa); } } } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/QualityTrimmer.java000066400000000000000000000216151247756524500252050ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.readers.QSeqReader; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import edu.msu.cme.rdp.readseq.writers.FastqWriter; import java.io.File; import java.io.FileInputStream; import java.util.zip.GZIPInputStream; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; /** * * @author fishjord */ public class QualityTrimmer { public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption("f", "fastq-out", false, "Write fastq instead of fasta file"); options.addOption("l", "less-than", false, "Trim at <= instead of strictly ="); options.addOption("i", "illumina", false, "Illumina trimming mode"); FastqWriter fastqOut = null; FastaWriter fastaOut = null; byte qualTrim = -1; boolean writeFasta = true; boolean trimle = false; boolean illumina = false; List readers = new ArrayList(); List seqFiles = new ArrayList(); try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("fastq-out")) { writeFasta = false; } if (line.hasOption("less-than")) { trimle = true; } if (line.hasOption("illumina")) { illumina = true; } args = line.getArgs(); if (args.length < 2) { throw new Exception("Unexpected number of arguments"); } if (args[0].length() != 1) { throw new Exception("Expected single character quality score"); } qualTrim = FastqCore.Phred33QualFunction.translate(args[0].charAt(0)); for (int index = 1; index < args.length; index++) { File seqFile = new File(args[index]); SeqReader reader; if (SeqUtils.guessFileFormat(seqFile) == SequenceFormat.FASTA) { if (index + 1 == args.length) { throw new Exception("Fasta files must be immediately followed by their quality file"); } File qualFile = new File(args[index + 1]); if (SeqUtils.guessFileFormat(qualFile) != SequenceFormat.FASTA) { throw new Exception(seqFile + " was not followed by a fasta quality file"); } reader = new QSeqReader(seqFile, qualFile); index++; } else { if(seqFile.getName().endsWith(".gz")) { reader = new SequenceReader(new GZIPInputStream(new FileInputStream(seqFile))); } else { reader = new SequenceReader(seqFile); } } readers.add(reader); seqFiles.add(seqFile); } } catch (Exception e) { new HelpFormatter().printHelp("USAGE: QualityTrimmer [options] [qual_file]", options, true); System.err.println("Error: " + e.getMessage()); System.exit(1); } for (int readerIndex = 0; readerIndex < readers.size(); readerIndex++) { File seqFile = seqFiles.get(readerIndex); String outStem = "trimmed_" + seqFile.getName().substring(0, seqFile.getName().lastIndexOf(".")); if (writeFasta) { fastaOut = new FastaWriter(outStem + ".fasta"); } else { fastqOut = new FastqWriter(outStem + ".fastq", FastqCore.Phred33QualFunction); } int[] lengthHisto = new int[200]; SeqReader reader = readers.get(readerIndex); QSequence qseq; long totalLength = 0; int totalSeqs = 0; long trimmedLength = 0; int trimmedSeqs = 0; int zeroLengthAfterTrimming = 0; long startTime = System.currentTimeMillis(); while ((qseq = (QSequence) reader.readNextSequence()) != null) { char[] bases = qseq.getSeqString().toCharArray(); byte[] qual = qseq.getQuality(); if (bases.length != qual.length) { System.err.println(qseq.getSeqName() + ": Quality length doesn't match seq length for seq"); continue; } totalSeqs++; totalLength += bases.length; int trimIndex = -1; if (illumina && qual[bases.length - 1] == qualTrim) { trimIndex = bases.length - 1; while (trimIndex >= 0 && qual[trimIndex] == qualTrim) { trimIndex--; } trimIndex++; //Technically we're positioned over the first good base, move back to the last bad base } else if (!illumina) { for (int index = 0; index < bases.length; index++) { if (qual[index] == qualTrim || (trimle && qual[index] < qualTrim)) { trimIndex = index; break; } } } String outSeq; byte[] outQual; if (trimIndex == -1) { outSeq = qseq.getSeqString(); outQual = qseq.getQuality(); } else { outSeq = new String(bases, 0, trimIndex); outQual = Arrays.copyOfRange(qual, 0, trimIndex); trimmedSeqs++; } int len = outSeq.length(); trimmedLength += len; if(len >= lengthHisto.length) { lengthHisto = Arrays.copyOf(lengthHisto, len + 1); } lengthHisto[len]++; if (outSeq.length() == 0) { //System.err.println(qseq.getSeqName() + ": length 0 after trimming"); zeroLengthAfterTrimming++; continue; } if (writeFasta) { fastaOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq); } else { fastqOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq, outQual); } } reader.close(); if (writeFasta) { fastaOut.close(); } else { fastqOut.close(); } System.out.println("Processed " + seqFile + " in " + (System.currentTimeMillis() - startTime) / 1000.0 + "s"); System.out.println("Before trimming:"); System.out.println("Total Sequences: " + totalSeqs); System.out.println("Total Sequence Data: " + totalLength); System.out.println("Average sequence length: " + ((float) totalLength / totalSeqs)); System.out.println(); System.out.println("After trimming:"); System.out.println("Total Sequences: " + (totalSeqs - zeroLengthAfterTrimming)); System.out.println("Sequences Trimmed: " + trimmedSeqs); System.out.println("Total Sequence Data: " + trimmedLength); System.out.println("Average sequence length: " + ((float) trimmedLength / (totalSeqs - zeroLengthAfterTrimming))); System.out.println(); System.out.println("Length\tCount"); for(int index = 0;index < lengthHisto.length;index++) { if(lengthHisto[index] == 0) { continue; } System.out.println(index + "\t" + lengthHisto[index]); } System.out.println(); System.out.println(); System.out.println(); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/ReferencePositionMapper.java000066400000000000000000000034331247756524500270030ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import java.io.File; /** * * @author fishjord */ public class ReferencePositionMapper { public static void main(String[] args) throws Exception { if(args.length != 1) { System.err.println("USAGE: ReferencePositionMapping "); System.exit(1); } SeqReader reader = new SequenceReader(new File(args[0])); Sequence refSeq = reader.readNextSequence(); char[] bases = refSeq.getSeqString().toCharArray(); int seqPos = 0; int modelPos = 0; for(int index = 0;index < bases.length;index++) { char b = bases[index]; if(Character.isLetter(b)) { seqPos++; System.err.println(seqPos + "\t" + modelPos); } if(Character.isUpperCase(b) || b == '-') { modelPos++; } } reader.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/ReferenceSeqHelper.java000066400000000000000000000062631247756524500257260ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.SeqFactory; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import java.io.InputStream; import java.util.HashMap; import java.util.Map; import java.util.Set; /** * * @author fishjord */ public class ReferenceSeqHelper { private Map> modelReferenceSeqMap = new HashMap(); private Map referenceSeqMap = new HashMap(); private static class ReferenceSeqHelperHolder { private static ReferenceSeqHelper helper = new ReferenceSeqHelper(); } public static ReferenceSeqHelper getInstance() { return ReferenceSeqHelperHolder.helper; } private ReferenceSeqHelper() { InputStream is = this.getClass().getResourceAsStream("/data/ref_seqs.fa"); if(is == null) throw new RuntimeException("Failed to find ref_seqs.fa in the data directory on the classpath"); try { SequenceReader seqReader = new SequenceReader(is); Sequence seq; while((seq = seqReader.readNextSequence()) != null) { modelReferenceSeqMap.put(seq.getSeqName(), SeqUtils.generateReferenceSeqMapping(seq.getSeqString())); referenceSeqMap.put(seq.getSeqName(), seq.getDesc()); } seqReader.close(); } catch(Exception e) { throw new RuntimeException("Fatal error reading ref_seq.fa", e); } } public String getRefSeq(String model) { return referenceSeqMap.get(model); } public Set getKnownModels() { return modelReferenceSeqMap.keySet(); } public Map getReferenceMap(String model) { return modelReferenceSeqMap.get(model); } public int translate(String model, int loc) { if(!modelReferenceSeqMap.containsKey(model)) throw new IllegalArgumentException("Unknown model '" + model + "'"); if(!modelReferenceSeqMap.get(model).containsKey(loc)) throw new IllegalArgumentException(loc + " isn't a model position"); return modelReferenceSeqMap.get(model).get(loc); } public int[] getEndPoints(String model, String seqString) { int[] modelEndPoints = SeqUtils.getSeqEndPoints(seqString); int refStart = translate(model, modelEndPoints[0]); int refEnd = translate(model, modelEndPoints[0]); return new int[] {refStart, refEnd}; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/ResampleSeqFile.java000066400000000000000000000201351247756524500252320ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.PrintStream; import java.util.HashSet; import java.util.Random; import java.util.Set; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; /** * * @author fishjord */ public class ResampleSeqFile { private static Random random = new Random(); private static final Options options = new Options(); static { options.addOption("n", "num-selection", true, "number of sequence to select for each sample. " + "Default is the smallest sample size. Limit to the default value."); options.addOption("s", "subregion_length", true, "If specified, radomly choose a subregion with the required length from the sequence. " + " If a selected sequence is shorter than the specified length, that sequence will not be included in the output, " + " which may result in not equal number of sequences in some samples."); } public static void select(String infiledir, String outdir, int num_of_seqs, int subregion_length)throws IOException{ File outdirFile = new File(outdir); if ( !outdirFile.exists()){ outdirFile.mkdir(); } File infile = new File(infiledir); // need to find the smallest sample size int min_num_of_seqs = Integer.MAX_VALUE; if ( infile.isDirectory() ) { for ( File f: infile.listFiles()){ IndexedSeqReader reader = new IndexedSeqReader(f); if ( reader.getSeqIdSet().size() < min_num_of_seqs){ min_num_of_seqs = reader.getSeqIdSet().size(); } } }else { IndexedSeqReader reader = new IndexedSeqReader(infile); if ( reader.getSeqIdSet().size() < min_num_of_seqs){ min_num_of_seqs = reader.getSeqIdSet().size(); } } if ( num_of_seqs == 0){ // if user dis not specify the number, use the minimum sample size num_of_seqs = min_num_of_seqs; } if ( min_num_of_seqs < num_of_seqs){ throw new IllegalArgumentException("The smallest sample size is " + min_num_of_seqs +". Please modify the value for option num_selection"); } String subregion = (subregion_length == 0) ? "": "_" + subregion_length + "bp"; if ( infile.isDirectory() ) { for ( File f: infile.listFiles()){ File outfile = new File( outdir, "subset_" + subregion + f.getName()); selectOne(f, num_of_seqs, subregion_length, outfile); } }else { String infile_prefix = infile.getName(); String infile_suffix = ""; int index = infile.getName().lastIndexOf("."); if ( index != -1){ infile_prefix = infile.getName().substring(0, index); infile_suffix = infile.getName().substring(index); } File outfile = new File( outdir, infile_prefix + ".sub" + subregion + infile_suffix); selectOne(infile, num_of_seqs, subregion_length, outfile); } } public static void selectOne(File infile, int num_of_seqs, int subregion_length, File outfile) throws IOException{ IndexedSeqReader reader = new IndexedSeqReader(infile); PrintStream out = new PrintStream(new FileOutputStream(outfile)); Object[] seqIdSet = reader.getSeqIdSet().toArray(); HashSet selectedIndexSet = randomSelectIndices(seqIdSet, num_of_seqs); // get the seq Sequence seq; if ( subregion_length == 0){ for ( int index: selectedIndexSet){ seq = reader.readSeq((String)seqIdSet[index]); out.println(">" + seqIdSet[index] + "\t" + seq.getDesc() + "\n" + seq.getSeqString()); } }else{ for ( int index: selectedIndexSet){ seq = reader.readSeq((String)seqIdSet[index]); if ( seq.getSeqString().length() >= subregion_length){ int rdmIndex = (int)(Math.floor(Math.random()* (seq.getSeqString().length() - subregion_length) )); out.println(">" + seqIdSet[index] + "\t" + seq.getDesc() + "\n" + seq.getSeqString().substring(rdmIndex, (rdmIndex+subregion_length)) ); } } } reader.close(); out.close(); } /** * random select (without replacement) a fraction of indices from an array * @param object[] * @param num_of_selection * @return * @throws IOException */ public static HashSet randomSelectIndices(Object[] seqIdSet, int num_of_selection) throws IOException{ int n = Math.min(num_of_selection, seqIdSet.length); HashSet selectedIndexSet = new HashSet(); while(selectedIndexSet.size() < n){ selectedIndexSet.add(random.nextInt(n)); } return selectedIndexSet; } /** * random select (without replacement) a fraction of sequence IDs from the input file * @param infile * @param fraction * @return * @throws IOException */ public static Set randomSelectSeq(File infile, float fraction) throws IOException{ IndexedSeqReader reader = new IndexedSeqReader(infile); Object[] seqIdSet = reader.getSeqIdSet().toArray(); int num_of_seqs = (int) (fraction * seqIdSet.length); HashSet selectedIndexSet = randomSelectIndices(seqIdSet, num_of_seqs); Set selectedSeqIDs = new HashSet(); for ( int index: selectedIndexSet){ selectedSeqIDs.add((String) seqIdSet[index]); } return selectedSeqIDs; } public static void main(String[] args) throws IOException{ int numOfSelection = 0; int subregion_length = 0; try{ CommandLine line = new PosixParser().parse(options, args); if ( line.hasOption("num-selection")){ numOfSelection = Integer.parseInt(line.getOptionValue("num-selection")); if ( numOfSelection < 1){ throw new Exception("num-selection should be at least 1"); } } if ( line.hasOption("subregion_length")){ subregion_length = Integer.parseInt(line.getOptionValue("subregion_length")); if ( subregion_length < 1){ throw new Exception("subregion_length should be at least 1"); } } args = line.getArgs(); if ( args.length != 2){ throw new Exception("Incorrect number of command line arguments"); } ResampleSeqFile.select(args[0], args[1], numOfSelection, subregion_length); }catch(Exception e){ new HelpFormatter().printHelp(120, "ResampleSeqFile [options] ", "", options, ""); System.out.println("ERROR: " + e.getMessage()); return; } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/RevComplement.java000066400000000000000000000124651247756524500250000ustar00rootroot00000000000000/* * To change this template, choose Tools | Templates * and open the template in the editor. */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.utils.orientation.OrientationChecker; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.PrintStream; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; /** * * @author wangqion */ public class RevComplement { private static final Options options = new Options(); static { options.addOption("i", "infile", true, "input fasta file"); options.addOption("o", "outfile", true, "output fasta file"); options.addOption("f", "format", true, "output format, fasta or fastq. Default is fasta"); options.addOption("c", "check", false, "If set, will check orientation of the rRNA sequenc, only reverse complement if needed"); } public static String revQualityString(String s){ StringBuilder qual = new StringBuilder(); for(char b: s.toCharArray()) { qual.insert(0,b); } return qual.toString(); } public static void main(String[] args) throws IOException { boolean checkOrientation = false; SequenceFormat outFormat = SequenceFormat.FASTA; File infile; File outfile ; try{ CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("check")) { checkOrientation = true; } if (line.hasOption("format")) { String f = line.getOptionValue("format"); if ( f.equalsIgnoreCase("fasta")){ outFormat = SequenceFormat.FASTA; } else if ( f.equalsIgnoreCase("fastq")){ outFormat = SequenceFormat.FASTQ; } else { throw new IllegalArgumentException("only fasta and fastq output are supported"); } } if (line.hasOption("infile")) { infile = new File(line.getOptionValue("infile")); }else { throw new Exception("infile is required"); } if (line.hasOption("outfile")) { outfile = new File(line.getOptionValue("outfile")); }else { throw new Exception("outfile is required"); } }catch (Exception e) { new HelpFormatter().printHelp(120, "RevComplement [options]", "", options, ""); System.err.println("ERROR: " + e.getMessage()); return; } OrientationChecker checker = OrientationChecker.getChecker(); SequenceFormat format = SeqUtils.guessFileFormat(infile); PrintStream out = new PrintStream(outfile); if ( format == SequenceFormat.FASTA ){ if ( outFormat == SequenceFormat.FASTQ){ throw new IllegalArgumentException("Can not ouput fastq when input is fasta"); } SequenceReader reader = new SequenceReader(infile); Sequence seq = null; while ( ( seq = reader.readNextSequence()) != null){ if ( checkOrientation) { if ( checker.isSeqReversed(seq.getSeqString())){ String checked_seqstring = IUBUtilities.reverseComplement(seq.getSeqString()); out.println(">" + seq.getSeqName() +"\t" + seq.getDesc() + "\trevcomp=TRUE"+ "\n" + checked_seqstring); }else { out.println(">" + seq.getSeqName() +"\t" + seq.getDesc()+ "\n" + seq.getSeqString()); } }else { out.println(">" + seq.getSeqName() +"\t" + seq.getDesc() + "\n" + IUBUtilities.reverseComplement(seq.getSeqString())); } } reader.close(); } else if ( format == SequenceFormat.FASTQ) { BufferedReader reader = new BufferedReader(new FileReader(infile)); String line = null; while ( (line=reader.readLine()) != null){ String seqID = line; String seqString = reader.readLine(); String qualID = reader.readLine(); String qualString = reader.readLine(); if ( checkOrientation) { if ( checker.isSeqReversed(seqString)){ seqString = IUBUtilities.reverseComplement(seqString); qualString = revQualityString(qualString); } }else { seqString = IUBUtilities.reverseComplement(seqString); qualString = revQualityString(qualString); } if ( outFormat == SequenceFormat.FASTQ){ out.println( seqID + "\n" + seqString + "\n+" + "\n" + qualString); }else { out.println( seqID + "\n" + seqString); } } } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/RmDupSeqs.java000066400000000000000000000141301247756524500240720ustar00rootroot00000000000000/* * Copyright (C) 2012 Michigan State University * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.util.HashMap; import java.util.HashSet; import java.util.Set; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; /** * * @author wangqion */ public class RmDupSeqs { private static final Options options = new Options(); static { options.addOption("i", "infile", true, "input fasta file"); options.addOption("o", "outfile", true, "output fasta file"); options.addOption("l", "min_seq_length", true, "filter sequence by minimum sequence length, default is 0"); options.addOption("d", "duplicates", false, "remove identical sequence, or sequence contained by another sequence"); options.addOption("g", "debug", false, "output the ids that are contained by other sequences to standard out"); } public static void filterDuplicates(String inFile, String outFile, int length, boolean debug) throws IOException{ HashMap idSet = new HashMap(); IndexedSeqReader reader = new IndexedSeqReader(new File(inFile)); BufferedWriter outWriter = new BufferedWriter(new FileWriter(new File(outFile))); Set allseqIDset = reader.getSeqIdSet(); Sequence seq; if ( debug){ System.out.println("ID\tdescription" + "\tcontained_by_ID\tdescription"); } for ( String id : allseqIDset) { seq = reader.readSeq(id); boolean dup = false; HashSet tempdupSet = new HashSet(); for ( String exID: idSet.keySet()){ String exSeq = idSet.get(exID); if ( exSeq.length() >= seq.getSeqString().length()){ if ( exSeq.contains(seq.getSeqString())){ dup = true; if ( debug){ Sequence temp = reader.readSeq(exID); System.out.println(id + "\t" + seq.getDesc() + "\t" + exID + "\t" + temp.getDesc()); } break; } }else if ( seq.getSeqString().contains(exSeq)){ tempdupSet.add(exID); } } if ( !dup){ idSet.put(id, seq.getSeqString()); } for ( String dupid: tempdupSet){ idSet.remove(dupid); if ( debug){ Sequence temp = reader.readSeq(dupid); System.out.println(dupid + "\t" + temp.getDesc() + "\t"+ id + "\t" + seq.getDesc()); } } } // get the unique seq for ( String id: idSet.keySet()){ seq = reader.readSeq(id); if ( seq.getSeqString().length() >= length){ outWriter.write(">" + id + "\t" + seq.getDesc() + "\n" + seq.getSeqString() + "\n"); } } reader.close(); outWriter.close(); } public static void filterByLength(String inFile, String outFile, int length) throws IOException{ SequenceReader seqReader = new SequenceReader(new File(inFile)); FastaWriter outWriter = new FastaWriter(outFile); Sequence seq = null; while ( (seq = seqReader.readNextSequence()) != null){ if ( seq.getSeqString().length() < length) { continue; } outWriter.writeSeq(seq.getSeqName(), seq.getDesc(), seq.getSeqString()); } seqReader.close(); outWriter.close(); } public static void main(String[] args) throws Exception{ String inFile; String outFile; int length = 0; boolean debug = false; boolean removeDuplicates = false; try{ CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("duplicates")) { removeDuplicates = true; } if (line.hasOption("min_seq_length")) { length = Integer.parseInt(line.getOptionValue("min_seq_length")); } if (line.hasOption("infile")) { inFile = line.getOptionValue("infile"); }else { throw new Exception("infile is required"); } if (line.hasOption("outfile")) { outFile = line.getOptionValue("outfile"); }else { throw new Exception("outfile is required"); } if (line.hasOption("debug")) { debug = true; } }catch (Exception e) { new HelpFormatter().printHelp(120, "RmRedundantSeqs [options]", "", options, ""); System.err.println("ERROR: " + e.getMessage()); return; } if ( !removeDuplicates){ filterByLength(inFile, outFile, length); }else { filterDuplicates(inFile, outFile, length, debug); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SFFConverter.java000066400000000000000000000067211247756524500245240ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import edu.msu.cme.rdp.readseq.writers.FastqWriter; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.readers.core.SFFCore; import java.io.File; import java.io.IOException; /** * * @author fishjord */ public class SFFConverter { public static void convert(File sffFile, File workDir, String outfilePrefix, SequenceFormat outFormat) throws IOException { if(outFormat == SequenceFormat.FASTA) { convertToFasta(sffFile, workDir, outfilePrefix); } else if(outFormat == SequenceFormat.FASTQ) { convertToFastq(sffFile, workDir, outfilePrefix); } else { throw new IOException("Unsupported target format " + outFormat); } } private static void convertToFasta(File sffFile, File workDir, String outfilePrefix) throws IOException { SFFCore core = new SFFCore(sffFile); FastaWriter fastaWriter = new FastaWriter(new File(workDir, outfilePrefix + ".fasta")); FastaWriter qualWriter = new FastaWriter(new File(workDir, outfilePrefix + ".qual")); QSequence seq; while ((seq = core.readNextSeq()) != null) { fastaWriter.writeSeq(seq); qualWriter.writeSeq(seq.getSeqName(), "", SeqUtils.translateQualString(seq.getQuality())); } qualWriter.close(); fastaWriter.close(); core.close(); } private static void convertToFastq(File sffFile, File workDir, String outfilePrefix) throws IOException { SFFCore core = new SFFCore(sffFile); FastqWriter fastqWriter = new FastqWriter(new File(workDir, outfilePrefix + ".fastq"), FastqCore.Phred33QualFunction); QSequence seq; while ((seq = core.readNextSeq()) != null) { fastqWriter.writeSeq(seq); } fastqWriter.close(); core.close(); } public static void main(String[] args) throws Exception { if (args.length != 3 && args.length != 4) { System.err.println("USAGE: SFFConverter [fasta|fastq] [workdir]"); return; } String format = args[0].toUpperCase(); File sffFile = new File(args[1]); String outfilePrefix = args[2]; File workdir = new File("."); if (args.length == 4) { workdir = new File(args[3]); } if (!format.equals("FASTA") && !format.equals("FASTQ")) { System.err.println("SFFConverter will only convert to fasta or fastq files"); return; } convert(sffFile, workdir, outfilePrefix, SequenceFormat.valueOf(format)); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SFFSplitter.java000066400000000000000000000203031247756524500243530ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.core.SFFCore; import edu.msu.cme.rdp.readseq.readers.core.SFFCore.CommonHeader; import edu.msu.cme.rdp.readseq.readers.core.SFFCore.ReadBlock; import edu.msu.cme.rdp.readseq.writers.SFFWriter; import java.io.File; import java.io.IOException; import java.io.RandomAccessFile; import java.io.FileReader; import java.io.BufferedReader; import java.io.FileWriter; import java.io.PrintWriter; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; /** * * @author fishjord */ public class SFFSplitter { public static void splitInto(File sffFile, Map barcodeToSample, File directory) throws IOException { SFFCore core = new SFFCore(sffFile); CommonHeader ch = core.getCommonHeader(); Map outputMap = new HashMap(); Map idOutputMap = new HashMap(); for (String sample : new HashSet(barcodeToSample.values())) { File outFile = new File(directory, sample + ".sff"); outputMap.put(sample, new SFFWriter(outFile, ch, core.getManifest())); // allow to append to existing seqid files if multiple tags belong to the same sample idOutputMap.put(sample, new PrintWriter(new FileWriter(new File(directory, sample + "_seqids.txt"), true))); } try { ReadBlock rb; for (int index = 0; index < ch.getNumReads(); index++) { rb = core.readReadBlock(); int left = Math.max(rb.getClipAdapterLeft(), rb.getClipQualLeft()); String trimmedSeq = rb.getSeq().substring(left - 1).toLowerCase(); //Biologists REALLY don't like zeros... //System.out.println(rb.getName() + "\t" + trimmedSeq.substring(0, 25) + "\t" + left); for (String barcode : barcodeToSample.keySet()) { //System.out.println("\t\t" + barcode); if (trimmedSeq.startsWith(barcode)) { String sample = barcodeToSample.get(barcode); outputMap.get(sample).writeReadBlock(rb); idOutputMap.get(sample).println(rb.getName()); break; } } } } finally { for (SFFWriter os : outputMap.values()) { os.close(); } for (PrintWriter out : idOutputMap.values()) { out.close(); } } } public static void dumpIndex(File f) throws Exception { SFFCore core = new SFFCore(f); RandomAccessFile tmp = new RandomAccessFile(f, "r"); tmp.seek(core.getCommonHeader().getIndexOffset()); int mftMagicNumber = 778921588; int srtMagicNumber = 779317876; int acceptedVersionMagicNumber = 825110576; int magicNumber = tmp.readInt(); if (magicNumber == mftMagicNumber) { System.out.println("Found an index header!"); int version = tmp.readInt(); if (version == acceptedVersionMagicNumber) { System.out.println("We've got a version we understand!"); int xmlSize = tmp.readInt(); int dataSize = tmp.readInt(); System.out.println("XML Size=" + xmlSize + ", dataSize=" + dataSize); byte[] xml = new byte[xmlSize]; tmp.read(xml); System.out.println(new String(xml)); } } else if (magicNumber == srtMagicNumber) { System.out.println("Found an index header!"); int version = tmp.readInt(); if (version == acceptedVersionMagicNumber) { System.out.println("We've got a version we understand!"); if (tmp.read() != 0) { throw new IOException("GAH NULL BYTE NOT FOUND OMG"); } } } else { throw new IOException("No supported index found"); } List currIndex = new ArrayList(); while (tmp.getFilePointer() != tmp.length()) { int b = tmp.readUnsignedByte(); if (b == 0xff) { byte[] nameArray = new byte[currIndex.size() - 5]; long indexLoc = 0; int[] multipliers = new int[]{0, 16581375, 65025, 255, 1}; for (int i = 0; i < currIndex.size(); i++) { if (i < nameArray.length) { nameArray[i] = (byte) (currIndex.get(i) & 0xff); } else { int index = i - nameArray.length; indexLoc += currIndex.get(i) * multipliers[index]; } } String name = new String(nameArray); System.out.println(name + "\t" + indexLoc); currIndex.clear(); } else { currIndex.add(b); } } } public static void main(String[] args) throws Exception { //dumpIndex(new File("/scratch/fishjord/test_sff/tuo.sff")); //dumpIndex(new File("/work/fishjord/other_projects/sra_submission/titanium_04222010/data/tmp/buk_region1.sff")); if (args.length != 3) { System.err.println("USAGE: SFFSplitter \n" + "Caution: The results will be appended the same files in the ouput_dir to if multiple barcodes map to the same sample."); return; } File inSff = new File(args[0]); File barcodeMappingFile = new File(args[1]); File outputDir = new File(args[2]); if (!outputDir.exists()) { if (!outputDir.mkdirs()) { System.err.println("Failed to make output dir " + outputDir); return; } } BufferedReader reader = new BufferedReader(new FileReader(barcodeMappingFile)); String line = ""; Map barcodeMap = new HashMap(); while ((line = reader.readLine()) != null) { String[] lexemes = line.trim().split("\\s+"); if (lexemes.length == 2) { if (barcodeMap.containsKey(lexemes[0])) { System.err.println("Warning: Duplicate mapping for " + lexemes[0] + " " + barcodeMap.get(lexemes[0]) + "," + lexemes[1]); } barcodeMap.put(lexemes[0].toLowerCase(), lexemes[1]); } } SFFSplitter.splitInto(inSff, barcodeMap, outputDir); /* //File inFile = new File("/work/fishjord/user_files/vamps_v6/clone43_culled3/derep/Clone43culled3.sff"); File inFile = new File("/scratch/fishjord/test_sff/tuo.sff"); //File inFile = new File("/scratch/fishjord/test_sff/out.sff"); //File inFile = new File("/scratch/wangqion/qiong_titanium/titanium_run_022010/sff/GB4XUSJ01.sff"); File outFile = new File("/scratch/fishjord/test_sff/out.sff"); long l = 55555; ByteBuffer bb = ByteBuffer.allocate(8); bb.putLong(l); for(byte b : bb.array()) { System.out.print(Integer.toHexString(b & 0xff) + " "); } System.out.println(); bb.rewind(); System.out.println(bb.getLong()); dumpIndex(inFile); //new SFFSplitter(inFile, new HashMap()).copyYo(outFile); //new SFFSplitter(inFile, new HashMap()).dumpIndex();*/ } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SeqFileIndexer.java000066400000000000000000000024101247756524500250540ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import java.io.File; import java.io.IOException; /** * * @author fishjord */ public class SeqFileIndexer { public static void main(String[] args) throws IOException { if(args.length != 2) { System.err.println("USAGE: SeqFileIndexer "); System.exit(1); } File inFile = new File(args[0]); File outFile = new File(args[1]); IndexedSeqReader.indexSeqFile(inFile, outFile); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SeqFileSplitter.java000066400000000000000000000057411247756524500252760ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import java.io.File; import java.io.IOException; import java.util.List; import java.util.ArrayList; /** * * @author fishjord */ public class SeqFileSplitter { public static List splitSeqFile(File seqFile, File outDir, int seqsPerSplit) throws IOException { if (!outDir.exists() && !outDir.mkdirs()) { throw new IOException("Output directory " + outDir + " doesn't exist and attempt to create failed"); } else if (!outDir.isDirectory()) { throw new IOException("Output directory " + outDir + " isn't a directory"); } SequenceReader seqReader = new SequenceReader(seqFile); FastaWriter out = null; List ret = new ArrayList(); try { int splitno = 0, seqsWritten = 0; String seqFileName = seqFile.getName(); File split = new File(outDir, (splitno++) + "_" + seqFileName); ret.add(split); out = new FastaWriter(split); Sequence seq; while ((seq = seqReader.readNextSequence()) != null) { if (seqsWritten >= seqsPerSplit) { out.close(); split = new File(outDir, (splitno++) + "_" + seqFileName); ret.add(split); out = new FastaWriter(split); seqsWritten = 0; } out.writeSeq(seq); seqsWritten ++; } return ret; } finally { seqReader.close(); if (out != null) { out.close(); } } } public static void main(String[] args) throws IOException { String usage = "Usage: SeqFileSplitter infile outdir seq_per_split"; if ( args.length != 3){ System.err.println(usage); return; } int seqpersplit = Integer.parseInt(args[2]); if ( seqpersplit < 1){ System.err.println(usage); return; } SeqFileSplitter.splitSeqFile(new File(args[0]), new File(args[1]), seqpersplit); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SeqUtils.java000066400000000000000000000454771247756524500240020ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.SequenceType; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.core.EMBLCore; import edu.msu.cme.rdp.readseq.readers.core.FastaCore; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.readers.core.GenbankCore; import edu.msu.cme.rdp.readseq.readers.core.SFFCore; import edu.msu.cme.rdp.readseq.readers.core.STKCore; import edu.msu.cme.rdp.readseq.readers.core.SeqReaderCore; import java.io.BufferedInputStream; import java.io.ByteArrayInputStream; import java.io.DataInputStream; import java.io.EOFException; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.IOException; import java.io.InputStream; import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; import java.util.zip.GZIPInputStream; /** * * @author fishjord */ public class SeqUtils { private static final List gapChars = Arrays.asList('.', '-', '~'); public static final int SFF_MAGIC_NUMBER = 779314790; public static final int SRF_MAGIC_NUMBER = 1397969478; public static final int STK_MAGIC_NUMBER = 589321044; public static final int GENBANK_MAGIC_NUMBER = 1280262997; public static final int EMBL_MAGIC_NUMBER = 1229201440; public static final Set RNAAlphabet = Collections.unmodifiableSet(new HashSet(Arrays.asList(new Character[]{ 'A', 'a', 'C', 'c', 'G', 'g', 'U', 'u', 'T', 't', 'M', 'm', 'R', 'r', 'W', 'w', 'S', 's', 'Y', 'y', 'K', 'k', 'B', 'b', 'H', 'h', 'V', 'v', 'D', 'd', 'N', 'n', 'I', 'i' }))); public static final Set proteinAlphabet = Collections.unmodifiableSet(new HashSet(Arrays.asList(new Character[]{ 'A', 'a', 'C', 'c', 'D', 'd', 'E', 'e', 'F', 'f', 'G', 'g', 'H', 'h', 'I', 'i', 'K', 'k', 'L', 'l', 'M', 'm', 'N', 'n', 'P', 'p', 'Q', 'q', 'R', 'r', 'S', 's', 'T', 't', 'V', 'v', 'W', 'w', 'Y', 'y', 'Z', 'z', 'B', 'b', 'X', 'x', 'u', 'U', 'j', 'J', '*' }))); public static final Set rrnaAmbiguity = Collections.unmodifiableSet(new HashSet(Arrays.asList(new Character[]{ 'y', 'Y', 'r', 'R', 'w', 'W', 's', 'S', 'k', 'K', 'm', 'M', 'd', 'D', 'v', 'V', 'h', 'H', 'b', 'B', 'x', 'X', 'n', 'N' }))); public static final Set proteinAmbiguity = Collections.unmodifiableSet(new HashSet(Arrays.asList(new Character[]{ 'x', 'X', '*' }))); public static final byte[] IUPAC = new byte[127]; public static final byte NON_COMPAREABLE = Byte.parseByte("0110" + "0000", 2); public static final byte A = (byte) (Byte.parseByte("0000" + "0001", 2)); public static final byte C = (byte) (Byte.parseByte("0000" + "0010", 2)); public static final byte G = (byte) (Byte.parseByte("0000" + "0100", 2)); public static final byte U = (byte) (Byte.parseByte("0000" + "1000", 2)); public static final byte AMB = Byte.parseByte("0010" + "0000", 2); public static final byte GAP = Byte.parseByte("0100" + "0000", 2); public static final byte Y = (byte) (C | U | AMB); public static final byte R = (byte) (A | G | AMB); public static final byte W = (byte) (A | U | AMB); public static final byte S = (byte) (G | C | AMB); public static final byte K = (byte) (G | U | AMB); public static final byte M = (byte) (A | C | AMB); public static final byte D = (byte) (A | G | U | AMB); public static final byte V = (byte) (A | G | C | AMB); public static final byte H = (byte) (A | C | U | AMB); public static final byte B = (byte) (G | C | U | AMB); public static final byte N = (byte) (A | C | G | U | AMB); static { for (int i = 0; i < IUPAC.length; ++i) { IUPAC[i] = -1; } IUPAC['A'] = IUPAC['a'] = A; IUPAC['C'] = IUPAC['c'] = C; IUPAC['G'] = IUPAC['g'] = G; IUPAC['U'] = IUPAC['u'] = IUPAC['T'] = IUPAC['t'] = U; IUPAC['M'] = M; IUPAC['R'] = R; IUPAC['W'] = W; IUPAC['S'] = S; IUPAC['Y'] = Y; IUPAC['K'] = K; IUPAC['V'] = V; IUPAC['H'] = H; IUPAC['D'] = D; IUPAC['B'] = B; IUPAC['-'] = GAP; IUPAC['.'] = GAP; IUPAC['~'] = GAP; IUPAC['N'] = N; IUPAC['X'] = N; IUPAC['m'] = IUPAC['M']; IUPAC['r'] = IUPAC['R']; IUPAC['w'] = IUPAC['W']; IUPAC['s'] = IUPAC['S']; IUPAC['y'] = IUPAC['Y']; IUPAC['k'] = IUPAC['K']; IUPAC['v'] = IUPAC['V']; IUPAC['h'] = IUPAC['H']; IUPAC['d'] = IUPAC['D']; IUPAC['b'] = IUPAC['B']; IUPAC['n'] = IUPAC['N']; IUPAC['x'] = IUPAC['X']; } public static byte[] toBytes(String seq) { byte[] seqBytes = new byte[seq.length()]; for (int col = 0; col < seq.length(); col++) { seqBytes[col] = SeqUtils.IUPAC[seq.charAt(col)]; } return seqBytes; } public static String fromBytes(byte[] bases) { StringBuilder ret = new StringBuilder(); for (byte base : bases) { if (base == A) { ret.append('A'); } else if (base == C) { ret.append('C'); } else if (base == G) { ret.append('G'); } else if (base == U) { ret.append('T'); } else if (base == GAP) { ret.append('-'); } else if (base == Y) { ret.append('Y'); } else if (base == R) { ret.append('R'); } else if (base == W) { ret.append('W'); } else if (base == S) { ret.append('S'); } else if (base == K) { ret.append('K'); } else if (base == M) { ret.append('M'); } else if (base == D) { ret.append('D'); } else if (base == V) { ret.append('V'); } else if (base == H) { ret.append('H'); } else if (base == B) { ret.append('B'); } else if (base == N) { ret.append('N'); } else { ret.append('?'); } } return ret.toString(); } public static Sequence getMaskedSeq(Sequence seq, char[] maskSeq) { return new Sequence(seq.getSeqName(), seq.getDesc(), getMaskedSeq(seq.getSeqString(), maskSeq)); } public static String getMaskedSeq(String bases, char[] maskSeq) { StringBuilder ret = new StringBuilder(); if (bases.length() != maskSeq.length) { System.err.println("\"" + bases + "\""); StringBuffer b = new StringBuffer(); for (char c : maskSeq) { b.append(c); } System.err.println("\"" + b + "\""); throw new IllegalArgumentException("Seq string[" + bases.length() + "] and mask string[" + maskSeq.length + "] are different lengths"); } for (int index = 0; index < maskSeq.length; index++) { if (maskSeq[index] != '0' && maskSeq[index] != '.' && maskSeq[index] != '~') { ret.append(bases.charAt(index)); } } return ret.toString(); } public static Sequence getMaskedBySeqString(Sequence seq) { return new Sequence(seq.getSeqName(), seq.getDesc(), getMaskedBySeqString(seq.getSeqString())); } public static String getMaskedBySeqString(String seqString) { StringBuilder ret = new StringBuilder(); char[] bases = seqString.toCharArray(); for (int index = 0; index < bases.length; index++) { if (bases[index] == '-' || Character.isUpperCase(bases[index])) { ret.append(bases[index]); } } return ret.toString(); } /** * Filters out gap characters if ignoreGaps is true and removes all white * space * * @param seqString * @param ignoreGaps * @return */ public static String filterSeqString(String seqString, boolean ignoreGaps) { StringBuilder ret = new StringBuilder(); for (char b : seqString.toCharArray()) { if (gapChars.contains(b) && ignoreGaps) { continue; } else if (!Character.isWhitespace(b)) { ret.append(b); } } return ret.toString(); } public static SeqReaderCore getSeqReaderCore(File f) throws IOException { SequenceFormat format = SeqUtils.guessFileFormat(f); SeqReaderCore core; if (format == SequenceFormat.GZIP) { return getSeqReaderCore(new GZIPInputStream(new FileInputStream(f))); } else if (format == SequenceFormat.FASTA) { core = new FastaCore(f); } else if (format == SequenceFormat.FASTQ) { core = new FastqCore(f); } else if (format == SequenceFormat.SFF) { core = new SFFCore(f); } else if (format == SequenceFormat.STK) { core = new STKCore(f); } else if (format == SequenceFormat.EMBL) { core = new EMBLCore(f); } else if (format == SequenceFormat.GENBANK) { core = new GenbankCore(f); } else if (format == SequenceFormat.EMPTY) { core = new SeqReaderCore.EmptyCore(f); } else { throw new IOException("Unable to process file format " + format); } return core; } public static SeqReaderCore getSeqReaderCore(InputStream is) throws IOException { BufferedInputStream in; if (is instanceof BufferedInputStream) { in = (BufferedInputStream) is; } else { in = new BufferedInputStream(is); } SequenceFormat format = SeqUtils.guessSequenceFormat(in); SeqReaderCore core; if (format == SequenceFormat.GZIP) { return getSeqReaderCore(new GZIPInputStream(is)); } else if (format == SequenceFormat.FASTA) { core = new FastaCore(in); } else if (format == SequenceFormat.FASTQ) { core = new FastqCore(in); } else if (format == SequenceFormat.SFF) { core = new SFFCore(in); } else if (format == SequenceFormat.EMBL) { core = new EMBLCore(in); } else if (format == SequenceFormat.GENBANK) { core = new GenbankCore(in); } else if (format == SequenceFormat.EMPTY) { core = new SeqReaderCore.EmptyCore(in); } else { throw new IOException("Unable to process file format " + format); } return core; } /** * Guess the file format for the given file * * @param f * @return */ public static SequenceFormat guessFileFormat(File f) throws IOException { if (!f.exists()) { throw new FileNotFoundException(f.getPath()); } if (f.length() == 0) { return SequenceFormat.EMPTY; } InputStream is = new FileInputStream(f); SequenceFormat format = guessSequenceFormat(new BufferedInputStream(is)); is.close(); return format; } public static SequenceFormat guessSequenceFormat(InputStream in) throws IOException { if (!in.markSupported()) { throw new IOException("Cannot test sequence format of an input stream that doesn't support marking"); } DataInputStream is = new DataInputStream(in); is.mark(4); try { int magicNumber = is.readInt(); switch (magicNumber) { case SFF_MAGIC_NUMBER: return SequenceFormat.SFF; case SRF_MAGIC_NUMBER: return SequenceFormat.SFF; case STK_MAGIC_NUMBER: return SequenceFormat.STK; case GENBANK_MAGIC_NUMBER: return SequenceFormat.GENBANK; case EMBL_MAGIC_NUMBER: return SequenceFormat.EMBL; } magicNumber >>= 16; if (((magicNumber >> 8) | ((magicNumber & 0xff) << 8)) == GZIPInputStream.GZIP_MAGIC) { return SequenceFormat.GZIP; } magicNumber >>= 8; //Shift us to the left most word hack to detect fasta/fastq that don't have a 4 byte magic number //Remember, an ascii character is 7 bits if (magicNumber == '>') { return SequenceFormat.FASTA; } else if (magicNumber == '@') { return SequenceFormat.FASTQ; } return SequenceFormat.UNKNOWN; } catch (EOFException e) { return SequenceFormat.EMPTY; } finally { is.reset(); } } public static SequenceType guessSequenceType(File f) throws IOException { SequenceReader reader = new SequenceReader(f); Sequence seq = reader.readNextSequence(); reader.close(); return guessSequenceType(seq); } public static SequenceType guessSequenceType(Sequence seq) { boolean canBeNucl = true; boolean canBeProt = true; for (char c : getUnalignedSeqString(seq.getSeqString()).toCharArray()) { if (!RNAAlphabet.contains(c)) { canBeNucl = false; } if (!proteinAlphabet.contains(c)) { canBeProt = false; } } if (canBeNucl) { return SequenceType.Nucleotide; } else if (canBeProt) { return SequenceType.Protein; } else { return SequenceType.Unknown; } } /** * Find the start and end points for an aligned sequence (first location of * a base) This method assumes that all non-model position gaps are the '.' * character * * @param seqString Sequence to test * @return 2 element array with the first element as the start and the * second element as the end (in model positions) */ public static int[] getSeqEndPoints(String seqString) { SequenceStats stats = new SequenceStats(seqString); return new int[]{stats.getStart(), stats.getEnd()}; } /** * Strips all gap characters ('.', '-', '~') and white space then lower * cases the supplied string to get the unaligned sequence * * @param seqString * @return */ public static String getUnalignedSeqString(String seqString) { return seqString.toLowerCase().replaceAll("[\\-\\.\\~\\s]", ""); } /** * Strips all gap characters ('.', '-', '~') and white space then lower * cases the supplied string to get the unaligned sequence * * @param seqString * @return */ public static Sequence getUnalignedSeq(Sequence seq) { return new Sequence(seq.getSeqName(), seq.getDesc(), getUnalignedSeqString(seq.getSeqString())); } /** * * Generates a mapping of model positions to reference sequence positions * * Model position start = 1 Ref sequence start = 1 * * @param referenceSeq * @return */ public static Map generateReferenceSeqMapping(String referenceSeq) { Map refMapping = new HashMap(); int modelPosition = 0; int refSeqPosition = 0; char[] bases = referenceSeq.toCharArray(); for (int index = 0; index < bases.length; index++) { char base = bases[index]; if (Character.isLetter(base)) { refSeqPosition++; } if (Character.isUpperCase(base) || base == '-') { modelPosition++; refMapping.put(modelPosition, refSeqPosition); } } return refMapping; } public static int countModelPositions(String seqString) { int count = 0; for (char b : seqString.toCharArray()) { if (Character.isUpperCase(b) || b == '-') { count++; } } return count; } /** * Turns an array of bytes in to a string of the numeric values they * represent * * @param qual * @return */ public static String translateQualString(byte[] qual) { StringBuilder ret = new StringBuilder(); for (byte c : qual) { ret.append(c).append(" "); } return ret.toString(); } public static int countSequences(List seqFiles) throws IOException { int seqCount = 0; Sequence seq; SeqReader reader; for (File file : seqFiles) { reader = null; try { reader = new SequenceReader(file); while ((seq = reader.readNextSequence()) != null) { if (!seq.getSeqName().startsWith("#")) { seqCount++; } } } catch (IOException e) { throw new IOException("Invalid sequence found in file " + file.getName()); } finally { if (reader != null) { reader.close(); } } } return seqCount; } public static void main(String[] args) throws IOException { DataInputStream dis = new DataInputStream(new ByteArrayInputStream("> ".getBytes())); int fasta = dis.readInt(); System.out.println(SeqUtils.guessFileFormat(new File("test/test.fa.gz"))); //System.out.println(fasta & 0xf0000000); System.out.println(fasta >> 24); System.out.println((int) '>'); dis = new DataInputStream(new ByteArrayInputStream("@ ".getBytes())); int fastq = dis.readInt(); //System.out.println(fastq & 0xf0000000); System.out.println(fastq >> 24); System.out.println((int) '@'); dis = new DataInputStream(new ByteArrayInputStream(">".getBytes())); System.out.println(dis.read()); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SequenceSelector.java000066400000000000000000000102011247756524500254530ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.core.FastqCore; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import edu.msu.cme.rdp.readseq.writers.FastqWriter; import edu.msu.cme.rdp.readseq.writers.SequenceWriter; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.util.HashSet; import java.util.Set; /** * * @author fishjord */ public class SequenceSelector { public static void main(String[] args) throws IOException { if (args.length < 5) { System.err.println("USAGE: SequenceSelector ids_file outfile outputformat keep[Y|N] seqfile(s) \n" + "Input format is fasta or fastq. The outputformat can be either fasta or fastq if inputs are fastq\n" + "Default is to keep the sequences in the ids_file. If keep is false or N, the sequences will be removed from output "); System.exit(1); } File idFile = new File(args[0]); SequenceWriter out = null; if ( args[2].equalsIgnoreCase("fasta")){ out = new FastaWriter(args[1]); } else if ( args[2].equalsIgnoreCase("fastq")){ out = new FastqWriter(args[1], FastqCore.Phred33QualFunction); } else { throw new IllegalArgumentException("only fasta and fastq output are supported"); } boolean keep = true; if ( args[3].equalsIgnoreCase("N") || args[3].equalsIgnoreCase("false")){ keep = false; } Set ids = new HashSet(); String line; BufferedReader reader = new BufferedReader(new FileReader(idFile)); while ((line = reader.readLine()) != null) { line = line.trim(); if (!line.equals("")) { String[] val = line.split("\\s+"); ids.add(val[0]); } } reader.close(); Sequence seq; boolean contains; HashSet foundIds = new HashSet(); for (int index = 4; index < args.length; index++) { SequenceReader seqReader = new SequenceReader(new File(args[index])); seq = seqReader.readNextSequence(); if ( (out instanceof FastqWriter) && !(seq instanceof QSequence) ) { throw new IllegalArgumentException("input file " + args[index] + " format is not fastq, can not write fastq output"); } contains = ids.contains(seq.getSeqName()); if ((contains && keep) || (!contains && !keep)) { out.writeSeq(seq); if ( keep){ foundIds.add(seq.getSeqName()); } } while ((seq = seqReader.readNextSequence()) != null) { contains = ids.contains(seq.getSeqName()); if ((contains && keep) || (!contains && !keep)) { out.writeSeq(seq); if ( keep ){ foundIds.add(seq.getSeqName()); if (foundIds.size() == ids.size()) { break; } } } } seqReader.close(); } out.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SequenceStats.java000066400000000000000000000036531247756524500250060ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; /** * * @author fishjord */ public class SequenceStats { private int start; private int end; private int modelPositions; private int length; public SequenceStats(String seqString) { start = -1; end = -1; int modelPosition = 0; length = 0; char[] bases = seqString.toCharArray(); for (int index = 0; index < bases.length; index++) { char base = bases[index]; if (Character.isUpperCase(base) || base == '-') { if(base != '-') modelPositions++; modelPosition++; } if (Character.isUpperCase(base)) { if (start == -1) { start = modelPosition; end = modelPosition; } else { end = modelPosition; } } } if(start != -1) length = end - start; } public int getEnd() { return end; } public int getLength() { return length; } public int getModelPositions() { return modelPositions; } public int getStart() { return start; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SequenceSummarizer.java000066400000000000000000000025701247756524500260430ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.util.HashMap; import java.util.Map; /** * * @author fishjord */ public class SequenceSummarizer { private Map lengthCounts = new HashMap(); public void addSequence(Sequence s) { int len = SeqUtils.getUnalignedSeqString(s.getSeqString()).length(); if(!lengthCounts.containsKey(len)) { lengthCounts.put(len, 0); } lengthCounts.put(len, lengthCounts.get(len) + 1); } public void addAlignedSequence(Sequence s) { } public static void main(String[] args) { } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/SequenceTrimmer.java000066400000000000000000000273031247756524500253250ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.readers.SeqReader; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.writers.FastaWriter; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.Arrays; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; import org.apache.commons.io.output.NullWriter; /** * * @author fishjord */ public class SequenceTrimmer { public enum CoordType { seq, model, alignment }; public static class TrimStats { /** Bases in the trimmed region */ char[] trimmedBases; /** First occupied model position (base 0) */ int seqStart = -1; /** Last occupied model position (base 0) */ int seqStop; /** Sequence position of the trim point (base 1) */ int seqTrimStart; /** Sequence position of the end point (base 1) */ int seqTrimStop; /** Length of the original sequence */ int seqLength; /** Length of the sequence after trimming */ int trimmedLength; /** Length of the model (used for sanity checking) */ int modelLength; /** Number of Ns in the sequence */ int numNs; /** Number of Ns in the trim region */ int nsInTrim; /** Filled model positions in the region */ float filledRatio; } private static Sequence readRefSeq(File refSeqFile) throws IOException { SeqReader reader = null; try { reader = new SequenceReader(refSeqFile); Sequence seq = reader.readNextSequence(); Sequence tmp = reader.readNextSequence(); if (tmp != null) { throw new IOException("Multiple sequences in refseq file"); } return seq; } catch (IOException e) { throw new IOException("Failed to read reference sequence from " + refSeqFile + ": " + e.getMessage(), e); } finally { if (reader != null) { try { reader.close(); } catch (IOException ignore) { } } } } public static TrimStats getStats(Sequence seq, int trimStart, int trimStop) { if(trimStart >= trimStop) { throw new IllegalArgumentException("Trim start has to come before trim end"); } TrimStats ret = new TrimStats(); int modelPos = 0; int seqPos = 0; int index; int filled = 0; char b; boolean ischar, isgap, ismodel, isupper, intrim; int alnStart = -1; char[] bases = seq.getSeqString().toCharArray(); for (index = 0; index < bases.length; index++) { b = bases[index]; ischar = Character.isLetter(b); isupper = ischar && Character.isUpperCase(b); isgap = !ischar && (b == '.' || b == '~' || b == '-'); ismodel = (b == '-') || isupper; intrim = (modelPos >= trimStart && modelPos < trimStop); if (ischar) { seqPos++; if(b == 'n' || b == 'N') { ret.numNs++; if(intrim) { ret.nsInTrim++; } } if(intrim) { ret.trimmedLength++; } } if (ismodel) { if(modelPos == trimStart) { ret.seqTrimStart = seqPos; alnStart = index; } if(modelPos >= trimStart && modelPos < trimStop) { filled++; if(ischar) { ret.filledRatio++; } } if(modelPos == trimStop) { ret.seqTrimStop = seqPos; ret.trimmedBases = Arrays.copyOfRange(bases, alnStart, index); } if(!isgap) { if(ret.seqStart == -1) { ret.seqStart = modelPos; } ret.seqStop = modelPos; } modelPos++; } } ret.seqLength = seqPos; ret.modelLength = modelPos; ret.filledRatio /= filled; return ret; } public static String trimMetaSeq(String seq, int trimStart, int trimStop) { int modelPos = 0; char[] bases = seq.toCharArray(); int start = 0, stop = 0; char b; for(int index = 0;index < bases.length;index++) { b = bases[index]; if(b == '.' || b == '~') { continue; } if(modelPos == trimStart) { start = index; } if(modelPos == trimStop) { stop = index; } modelPos++; } if(stop == 0) { stop = bases.length; } return new String(Arrays.copyOfRange(bases, start, stop)); } public static int translateCoord(int coord, Sequence seq, CoordType in, CoordType out) { int modelPos = 0; int seqPos = 0; int index; char[] bases = seq.getSeqString().toCharArray(); for (index = 0; index < bases.length; index++) { if (Character.isLetter(bases[index])) { seqPos++; } if ((in == CoordType.seq && seqPos == coord) || (in == CoordType.model && modelPos == coord) || (in == CoordType.alignment && index == coord)) { break; } if (bases[index] == '-' || Character.isUpperCase(bases[index])) { modelPos++; } } switch (out) { case seq: return seqPos; case model: return modelPos; case alignment: return index; } throw new IllegalArgumentException("Dunno what to do with out value " + out); } public static boolean didSeqPass(TrimStats stats, int minLength, int minTrimLength, int maxNs, int maxTrimNs, float minFilledRatio) { if(stats.trimmedLength <= minTrimLength) { return false; } if(stats.trimmedLength <= minLength) { return false; } if(stats.numNs > maxNs) { return false; } if(stats.nsInTrim > maxTrimNs) { return false; } if(stats.filledRatio < minFilledRatio) { return false; } return true; } public static void writeStatsHeader(PrintWriter out) { out.println("#seq name\tfirst model pos\tlast model pos\tfilled ratio\ttrim seq start coord\ttrim seq end coord\tNs\tNs in trimmed seq\ttrimmed seq length\tseq length\tpassed trimming"); } public static void writeStats(PrintWriter out, String seqName, TrimStats stats, boolean passed) { out.println(String.format("%s\t%d\t%d\t%.2f\t%d\t%d\t%d\t%d\t%d\t%d\t%b", seqName, stats.seqStart, stats.seqStop, stats.filledRatio, stats.seqTrimStart, stats.seqTrimStop, stats.numNs, stats.nsInTrim, stats.trimmedLength, stats.seqLength, passed)); } public static void main(String[] args) throws IOException { Options options = new Options(); options.addOption("r", "ref-seq", true, "Trim points are given as positions in a reference sequence from this file"); options.addOption("i", "inclusive", false, "Trim points are inclusive"); options.addOption("l", "length", true, "Minimum length of sequence after trimming"); options.addOption("f", "filled-ratio", true, "Minimum ratio of filled model positions of sequence after trimming"); options.addOption("o", "out", true, "Write sequences to directory (default=cwd)"); options.addOption("s", "stats", true, "Write stats to file"); PrintWriter statsOut = new PrintWriter(new NullWriter()); boolean inclusive = false; int minLength = 0; int minTrimmedLength = 0; int maxNs = 0; int maxTrimNs = 0; int trimStart = 0; int trimStop = 0; Sequence refSeq = null; float minFilledRatio = 0; int expectedModelPos = -1; String[] inputFiles = null; File outdir = new File("."); try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("ref-seq")) { refSeq = readRefSeq(new File(line.getOptionValue("ref-seq"))); } if (line.hasOption("inclusive")) { inclusive = true; } if (line.hasOption("length")) { minLength = Integer.valueOf(line.getOptionValue("length")); } if (line.hasOption("filled-ratio")) { minFilledRatio = Float.valueOf(line.getOptionValue("filled-ratio")); } if (line.hasOption("out")) { outdir = new File(line.getOptionValue("out")); if(!outdir.isDirectory()) { outdir = outdir.getParentFile(); System.err.println("Output option is not a directory, using " + outdir + " instead"); } } if (line.hasOption("stats")) { statsOut = new PrintWriter(line.getOptionValue("stats")); } args = line.getArgs(); if (args.length < 3) { throw new Exception("Unexpected number of arguments"); } trimStart = Integer.parseInt(args[0]); trimStop = Integer.parseInt(args[1]); inputFiles = Arrays.copyOfRange(args, 2, args.length); if (refSeq != null) { expectedModelPos = SeqUtils.getMaskedBySeqString(refSeq.getSeqString()).length(); trimStart = translateCoord(trimStart, refSeq, CoordType.seq, CoordType.model); trimStop = translateCoord(trimStop, refSeq, CoordType.seq, CoordType.model); } } catch (Exception e) { new HelpFormatter().printHelp("SequenceTrimmer ...", options); System.err.println("Error: " + e.getMessage()); } System.err.println("Starting sequence trimmer"); System.err.println("* Input files: " + Arrays.asList(inputFiles)); System.err.println("* Minimum Length: " + minLength); System.err.println("* Trim point inclusive?: " + inclusive); System.err.println("* Trim points: " + trimStart + "-" + trimStop); System.err.println("* Min filled ratio: " + minFilledRatio); System.err.println("* refSeq: " + ((refSeq == null) ? "model" : refSeq.getSeqName() + " " + refSeq.getDesc())); Sequence seq; SeqReader reader; TrimStats stats; writeStatsHeader(statsOut); FastaWriter seqWriter; File in; for (String infile : inputFiles) { in = new File(infile); reader = new SequenceReader(in); seqWriter = new FastaWriter(new File(outdir, "trimmed_" + in.getName())); while ((seq = reader.readNextSequence()) != null) { if(seq.getSeqName().startsWith("#")) { seqWriter.writeSeq(seq.getSeqName(), "", trimMetaSeq(seq.getSeqString(), trimStart, trimStop)); continue; } stats = getStats(seq, trimStart, trimStop); boolean passed = didSeqPass(stats, minLength, minTrimmedLength, maxNs, maxTrimNs, minFilledRatio); writeStats(statsOut, seq.getSeqName(), stats, passed); if(passed) { seqWriter.writeSeq(seq.getSeqName(), seq.getDesc(), new String(stats.trimmedBases)); } } reader.close(); seqWriter.close(); } statsOut.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/000077500000000000000000000000001247756524500231415ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/ComplementRegion.java000066400000000000000000000040751247756524500272610ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import edu.msu.cme.rdp.readseq.utils.IUBUtilities; /** * * @author fishjord */ public class ComplementRegion extends SingleSeqRegion { private SingleSeqRegion complementOf; public ComplementRegion(SingleSeqRegion complementOf) { if(complementOf == null) throw new IllegalArgumentException("ComplementOf must not be null"); this.complementOf = complementOf; } public SingleSeqRegion getComplementOf() { return complementOf; } @Override public String toString() { return "complement(" + complementOf.toString() + ")"; } @Override public String getId() { return complementOf.getId(); } @Override public int getSeqStart() { return complementOf.getSeqStart(); } @Override public int getSeqStop() { return complementOf.getSeqStop(); } @Override public String getSeqRegion(String seq, int offset) { return IUBUtilities.reverseComplement(complementOf.getSeqRegion(seq, offset)); } @Override public Extends getExtends() { Extends e = complementOf.getExtends(); if(e == Extends.BEYOND_BEGIN) return Extends.BEYOND_END; else if(e == Extends.BEYOND_END) return Extends.BEYOND_BEGIN; else return e; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/Extends.java000066400000000000000000000015421247756524500254200ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; /** * * @author fishjord */ public enum Extends { EXACT, BEYOND_BEGIN, BEYOND_END, BEYOND_BOTH } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/JoinRegion.java000066400000000000000000000062101247756524500260460ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import java.util.List; /** * * @author fishjord */ public class JoinRegion extends SingleSeqRegion { private List joinRegions; private String id = null; private boolean isOrder; private int smallestStart = Integer.MAX_VALUE; private int largestStop = Integer.MIN_VALUE; public JoinRegion(String id, List joinRegions, boolean isOrder) { if(joinRegions == null || joinRegions.size() < 2) { throw new IllegalArgumentException("JoinRegions must join at least 2 regions"); } for(SingleSeqRegion region : joinRegions) { if(region.getSeqStart() < smallestStart) smallestStart = region.getSeqStart(); if(region.getSeqStop() > largestStop) largestStop = region.getSeqStop(); } this.id = id; this.joinRegions = joinRegions; } public List getJoinRegions() { return joinRegions; } @Override public String toString() { String ret = ""; if(isOrder) { ret = "order("; } else { ret = "join("; } for(SingleSeqRegion r : joinRegions) { ret += r.toString() + ","; } return ret.substring(0, ret.length() - 1) + ")"; } @Override public String getId() { return id; } @Override public int getSeqStart() { return smallestStart; } @Override public int getSeqStop() { return largestStop; } @Override public String getSeqRegion(String seq, int offset) { StringBuffer ret = new StringBuffer(); for(SingleSeqRegion region : joinRegions) { ret.append(region.getSeqRegion(seq, offset)); } return ret.toString(); } @Override public Extends getExtends() { Extends ret = Extends.EXACT; if(joinRegions.size() > 0) { Extends e = joinRegions.get(0).getExtends(); if(e == Extends.BEYOND_BEGIN || e == Extends.BEYOND_BOTH) { ret = Extends.BEYOND_BEGIN; } e = joinRegions.get(joinRegions.size() - 1).getExtends(); if(e == Extends.BEYOND_END || e == Extends.BEYOND_BOTH) { if(ret == Extends.EXACT) { ret = Extends.BEYOND_END; } else { ret = Extends.BEYOND_BOTH; } } } return ret; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/RegionParser.java000066400000000000000000000154351247756524500264140ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import java.io.IOException; import java.io.StringReader; import java.util.ArrayList; import java.util.List; /** * * @author fishjord */ public class RegionParser { final static String accnoGiPattern = "(\\d+)|([A-Z_]+\\d+(\\.\\d+)?)|(gi\\|\\d+)"; public static SingleSeqRegion parse(String regionString) throws IOException { StringReader reader = new StringReader(regionString.replaceAll("\\s+", "")); return parseRegion(reader); } private static SingleSeqRegion parseRegion(StringReader in) throws IOException { IdentifierOrRange idOrRange = parseIdentifierOrRange(in); if (idOrRange.identifier == null) { GBRange range = idOrRange.range; return new SimpleRegion("", range.rangeStart, range.rangeEnd, range.rangeExtends); } else { String identifier = idOrRange.identifier; if (identifier.equals("join") || identifier.equals("order")) { return parseJoin(in, identifier.equals("order")); } else if (identifier.equals("complement")) { return parseComplement(in); } else if (identifier.matches(accnoGiPattern)) { idOrRange = parseIdentifierOrRange(in); GBRange range = idOrRange.range; if (range == null) { throw new IOException("Fatal error when trying to parse range \"" + idOrRange.identifier + "\""); } return new SimpleRegion(identifier, range.rangeStart, range.rangeEnd, range.rangeExtends); } else { throw new IOException("Unexpected token \"" + identifier + "\""); } } } private static SingleSeqRegion parseJoin(StringReader in, boolean isOrder) throws IOException { List joinOf = new ArrayList(); String id = null; while (true) { SingleSeqRegion r = parseRegion(in); if (id == null || id.isEmpty()) { id = r.getId(); } else if (!id.equals(r.getId()) && !r.getId().isEmpty()) { throw new IOException("SingleSeqRegion can only handle sequences of...a single seq..."); } joinOf.add(r); int n = in.read(); if (n == -1) { throw new IOException("Malformed join statement buffer=" + joinOf); } char c = (char) n; if (c == ')') { return new JoinRegion(id, joinOf, isOrder); } else if (c != ',') { throw new IOException("Unexpected '" + c + "\' in join, buffer=" + joinOf); } } } private static SingleSeqRegion parseComplement(StringReader in) throws IOException { SingleSeqRegion ret = new ComplementRegion(parseRegion(in)); int next = in.read(); if (next == -1) { throw new IOException("Unexpected end of region, last region= " + ret.toString()); } if (next != ')') { throw new IOException("Unexpected '" + (char) next + "', last region= " + ret.toString()); } return ret; } private static class IdentifierOrRange { String identifier; GBRange range; } private static class GBRange { public int rangeStart; public int rangeEnd; public Extends rangeExtends; } private static IdentifierOrRange parseIdentifierOrRange(StringReader in) throws IOException { IdentifierOrRange ret = new IdentifierOrRange(); StringBuilder buf = new StringBuilder(); int i; Extends e = Extends.EXACT; int rangeStart, rangeEnd; in.mark(1); char c = (char) in.read(); if (c == '<') { e = Extends.BEYOND_BEGIN; } else { buf.append(c); } in.mark(1); while ((i = in.read()) != -1) { c = (char) i; if (c == ',' || c == ')') { in.reset(); break; } if (c == ':' || c == '(' || c == '.') { break; } buf.append(c); in.mark(1); } boolean isIdentifier = false; if (c == ':' || c == '(') { //So we know if we see a : or a ( we've got an identifier, think 'join(', 'complement(', 'AHQ000:' isIdentifier = true; } else if (c == '.' && (c = (char) in.read()) != '.') { //If we didn't see a : or ( but we saw a . we could be parsing a range, or it could still be an identifier, if the following character is a '.' it has to be a range, think 123..456, otherwise just treat it as an id isIdentifier = true; buf.append('.').append(c); while ((i = in.read()) != -1) { c = (char) i; if (c == ':' || c == '(') { break; } buf.append(c); } } if (isIdentifier) { if (e == Extends.BEYOND_BEGIN) { buf.insert(0, "<"); } ret.identifier = buf.toString(); return ret; } rangeStart = new Integer(buf.toString()); if(c != ',' && c != ')') { buf = new StringBuilder(); c = (char) in.read(); if (c == '>') { if (e == Extends.BEYOND_BEGIN) { e = Extends.BEYOND_BOTH; } else { e = Extends.BEYOND_END; } } else { buf.append(c); } in.mark(1); while ((i = in.read()) != -1) { c = (char) i; if (c == ',' || c == ')') { in.reset(); break; } if (!Character.isDigit(c)) { throw new IOException("Expected digit in range, not " + c); } buf.append(c); in.mark(1); } } rangeEnd = new Integer(buf.toString()); GBRange range = new GBRange(); range.rangeStart = rangeStart; range.rangeEnd = rangeEnd; range.rangeExtends = e; ret.range = range; return ret; } public static void main(String[] args) throws IOException { for(String s : args) { System.out.println(s); System.out.println(parse(s)); System.out.println(); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/SimpleRegion.java000066400000000000000000000046721247756524500264120ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; /** * * @author fishjord */ public class SimpleRegion extends SingleSeqRegion { private String id; private int seqStart; private int seqStop; private Extends e; public SimpleRegion(String id, int start, int stop, Extends e) { this.id = id; if(start < stop) { this.seqStart = start; this.seqStop = stop; } else { this.seqStart = stop; this.seqStop = start; } this.e = e; } @Override public String toString() { String ret = ""; if(id != null && !id.equals("")) { ret += id + ":"; } if(seqStart == seqStop) { if(e == Extends.BEYOND_BEGIN) { ret += "<"; } else if(e == Extends.BEYOND_END) { ret += ">"; } ret += seqStart; } else { if(e == Extends.BEYOND_BEGIN || e == Extends.BEYOND_BOTH) { ret += "<"; } ret += seqStart + ".."; if(e == Extends.BEYOND_END || e == Extends.BEYOND_BOTH) { ret += ">"; } if(seqStart != seqStop) { ret += seqStop; } } return ret; } public String getId() { return id; } @Override public int getSeqStart() { return seqStart; } @Override public int getSeqStop() { return seqStop; } @Override public String getSeqRegion(String seq, int offset) { if(seqStart < offset) throw new IllegalArgumentException("Seq's offset (" + offset + ") is more than my start (" + seqStart + ") [" + this.toString() + "]"); return seq.substring(seqStart - offset, seqStop - offset + 1); } @Override public Extends getExtends() { return e; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/gbregion/SingleSeqRegion.java000066400000000000000000000022571247756524500270500ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import java.io.Serializable; /** * * @author fishjord */ public abstract class SingleSeqRegion implements Serializable { public abstract String getId(); public abstract int getSeqStart(); public abstract int getSeqStop(); public abstract String getSeqRegion(String seq, int offset); public abstract Extends getExtends(); public String getSeqRegion(String seq) { return getSeqRegion(seq, 1); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/kmermatch/000077500000000000000000000000001247756524500233205ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/kmermatch/KmerMatchCore.java000066400000000000000000000027221247756524500266520ustar00rootroot00000000000000/* * To change this template, choose Tools | Templates * and open the template in the editor. */ package edu.msu.cme.rdp.readseq.utils.kmermatch; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.io.IOException; import java.util.ArrayList; import java.util.Comparator; /** * * @author wangqion */ public abstract class KmerMatchCore { public static class ResultComparator implements Comparator { public int compare(Object a, Object b){ if ( ((BestMatch)a).sab < ((BestMatch)b).sab){ return 1; }else { if ( ((BestMatch)a).sab > ((BestMatch)b).sab){ return -1; }else { return ((BestMatch)a).match.getSeqName().compareTo(((BestMatch)b).match.getSeqName()); } } } } public static class BestMatch{ Sequence match; float sab; boolean revComp ; BestMatch(Sequence s, float score, boolean r){ match = s; sab = score; revComp = r; } public Sequence getBestMatch(){ return match; } public boolean isRevComp(){ return revComp; } public float getSab(){ return sab; } } public abstract ArrayList findTopKMatch(Sequence seq, int k) throws IOException; } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/kmermatch/NuclSeqMatch.java000066400000000000000000000133271247756524500265200ustar00rootroot00000000000000/* * Copyright (C) 2014 rdpstaff * */ package edu.msu.cme.rdp.readseq.utils.kmermatch; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator; import java.io.File; import java.io.IOException; import java.io.PrintStream; import java.util.ArrayList; import java.util.BitSet; import java.util.HashMap; import java.util.List; import java.util.TreeSet; /** * * @author wangqion */ public class NuclSeqMatch extends KmerMatchCore { static class WordSequence{ Sequence seq; BitSet bitset = new BitSet(getSetSize()); WordSequence(Sequence s){ seq = s; } } private static int setsize ; //key is the seqID, value is the unique integer kmer set private HashMap seqWordMap = new HashMap (); public NuclSeqMatch(String seqfile, int wordSize) throws IOException { if ( !GoodWordIterator.isWordsizeHasSet()){ GoodWordIterator.setWordSize(wordSize); } setsize = (int) Math.pow(4, GoodWordIterator.getWordsize() ); SequenceReader parser = new SequenceReader(new File(seqfile)); Sequence seq; while ( (seq = parser.readNextSequence()) != null) { GoodWordIterator generator = new GoodWordIterator(seq.getSeqString()); WordSequence wordSeq = new WordSequence(seq); while ( generator.hasNext()){ wordSeq.bitset.set(generator.next()); } seqWordMap.put(seq.getSeqName(), wordSeq); } parser.close(); } public NuclSeqMatch(String seqfile) throws IOException { this(seqfile, GoodWordIterator.DEFAULT_WORDSIZE); } public NuclSeqMatch(List refSeqs) throws IOException{ this(refSeqs, GoodWordIterator.DEFAULT_WORDSIZE); } public NuclSeqMatch(List refSeqs, int wordSize) throws IOException{ if ( !GoodWordIterator.isWordsizeHasSet()){ GoodWordIterator.setWordSize(wordSize); } for (Sequence seq: refSeqs){ GoodWordIterator generator = new GoodWordIterator(seq.getSeqString()); WordSequence wordSeq = new WordSequence(seq); while ( generator.hasNext()){ wordSeq.bitset.set(generator.next()); } seqWordMap.put(seq.getSeqName(), wordSeq); } } protected static int getSetSize(){ return setsize; } public TreeSet findAllMatches(Sequence query) throws IOException{ WordSequence queryWordSeq = seqWordMap.get(query.getSeqName()); if ( queryWordSeq == null){ queryWordSeq = new WordSequence(query); GoodWordIterator generator = new GoodWordIterator(query.getSeqString()); while ( generator.hasNext()){ queryWordSeq.bitset.set(generator.next()); } } TreeSet orderedResultSet = new TreeSet( new ResultComparator()); BitSet queryWordSet = queryWordSeq.bitset; BitSet tempQuerySet; float queryWordSize = queryWordSet.cardinality(); for ( String train: seqWordMap.keySet()){ tempQuerySet = (BitSet) queryWordSet.clone(); BitSet trainWordSet = seqWordMap.get(train).bitset; int trainWordSize = trainWordSet.cardinality(); float minWordCount = queryWordSize <= trainWordSize? queryWordSize: trainWordSize; tempQuerySet.and(trainWordSet); orderedResultSet.add( new BestMatch(seqWordMap.get(train).seq, tempQuerySet.cardinality()/minWordCount, false)); //System.out.println(query.getSeqName() + "\t" + train + "\t" + tempQuerySet.cardinality() + "\t" + minWordCount + "\t" + (Math.round(100*tempQuerySet.cardinality()/minWordCount))); } return orderedResultSet; } public ArrayList findTopKMatch(Sequence query, int k) throws IOException{ TreeSet orderedResultSet = findAllMatches(query); ArrayList topkMatchList = new ArrayList(); for ( BestMatch m: orderedResultSet){ if ( topkMatchList.size() < k) topkMatchList.add(m); } return topkMatchList; } public static void main(String[] args) throws IOException{ String usage = "nucl_ref.fa nucl_query.fa outFile word_size knn\n" + " This program takes a nucleotide query sequence file, returns the top k best matching nucleotide reference sequences based on nucleotide kmer matching \n" + " word_size 8 is recommended for the best performance. Range from 6 to 10 is recommended.\n" ; if ( args.length != 5) { System.err.println(usage); System.exit(1); } // need to set the word size int wordSize = Integer.parseInt(args[3]); KmerMatchCore theObj = new NuclSeqMatch(args[0], wordSize); PrintStream out = new PrintStream(args[2]); int k = Integer.parseInt(args[4]); SequenceReader parser = new SequenceReader(new File(args[1])); Sequence seq; while ( (seq = parser.readNextSequence()) != null) { ArrayList matches = theObj.findTopKMatch(seq, k); for ( BestMatch match: matches){ out.println(seq.getSeqName() + "\t" + match.getBestMatch().getSeqName() + "\t" + match.getSab() + "\t" + match.getBestMatch().getDesc()); } } parser.close(); out.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/kmermatch/ProteinSeqMatch.java000066400000000000000000000144711247756524500272400ustar00rootroot00000000000000/* * Copyright (C) 2014 rdpstaff * */ package edu.msu.cme.rdp.readseq.utils.kmermatch; import edu.msu.cme.rdp.readseq.SequenceType; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import edu.msu.cme.rdp.readseq.utils.IUBUtilities; import edu.msu.cme.rdp.readseq.utils.SeqUtils; import edu.msu.cme.rdp.readseq.utils.orientation.ProteinWordGenerator; import java.io.File; import java.io.IOException; import java.io.PrintStream; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.TreeSet; import java.util.concurrent.ConcurrentHashMap; /** * * @author wangqion */ public class ProteinSeqMatch extends KmerMatchCore{ private ConcurrentHashMap> refWordMap = new ConcurrentHashMap>(); private ConcurrentHashMap refSeqMap = new ConcurrentHashMap(); private ProteinWordGenerator proteinWordGenerator = null; private static final float SabThreshold = 0.6f; // public ProteinSeqMatch(String seqFile, int wordSize) throws IOException { proteinWordGenerator = new ProteinWordGenerator(wordSize); SequenceReader parser = new SequenceReader(new File(seqFile)); Sequence seq; while ( (seq = parser.readNextSequence()) != null) { addRefSeq(seq); } parser.close(); } public ProteinSeqMatch(String seqFile) throws IOException { this(seqFile, ProteinWordGenerator.WORDSIZE); } public ProteinSeqMatch(List refSeqs, int wordSize){ proteinWordGenerator = new ProteinWordGenerator(wordSize); // initialize the protein words for (Sequence seq: refSeqs){ addRefSeq(seq); } } public synchronized void addRefSeq(Sequence seq){ refSeqMap.put(seq.getSeqName(), seq); refWordMap.put(seq.getSeqName(), proteinWordGenerator.parseProtein(SeqUtils.getUnalignedSeqString(seq.getSeqString())) ); } /* * This program take a nucleotide or protein sequence, returns the top k best matching reference sequences * If it's nucleotide sequence, translates to three protein sequence strings, one for each frame. * It then calclates the sab score (shared protein kmers) between query and each reference seq. * The above process is repeated for the reverse orientation. */ public ArrayList findTopKMatch(Sequence seq, int k){ TreeSet orderedResultSet = new TreeSet( new ResultComparator()); SequenceType seqtype = SeqUtils.guessSequenceType(seq); HashSet queryWordSet; float queryWordSize; if (seqtype == SequenceType.Nucleotide){ queryWordSet = proteinWordGenerator.parseNuclAllFrames(seq.getSeqString()); // we need to divide the query word size by three since we have words from three frames queryWordSize = queryWordSet.size()/3f; } else { queryWordSet = proteinWordGenerator.parseProtein(seq.getSeqString()); queryWordSize = queryWordSet.size(); } float tempBestSab = 0; HashSet targetWordSet ; for ( Sequence target: refSeqMap.values()){ targetWordSet = refWordMap.get(target.getSeqName()); HashSet tempSet = new HashSet(); tempSet.addAll(queryWordSet); float minWordCount = queryWordSize<= targetWordSet.size()? queryWordSize: targetWordSet.size(); tempSet.retainAll(targetWordSet); float sab = tempSet.size()/minWordCount; if ( sab >= tempBestSab){ tempBestSab = sab; } orderedResultSet.add( new BestMatch(target, sab, false)); } if(seqtype == SequenceType.Nucleotide && tempBestSab < this.SabThreshold) { // check reverse queryWordSet = proteinWordGenerator.parseNuclAllFrames( IUBUtilities.reverseComplement(seq.getSeqString()) ); for ( Sequence target: refSeqMap.values()){ targetWordSet = refWordMap.get(target.getSeqName()); HashSet tempSet = new HashSet(); tempSet.addAll(queryWordSet); float minWordCount = queryWordSize<= targetWordSet.size()? queryWordSize: targetWordSet.size(); tempSet.retainAll(targetWordSet); float sab = tempSet.size()/minWordCount; orderedResultSet.add( new BestMatch(target, sab, true)); } } ArrayList topkMatchList = new ArrayList(); for ( BestMatch m: orderedResultSet){ if ( topkMatchList.size() < k) topkMatchList.add(m); } return topkMatchList; } public static void main (String[] args ) throws IOException{ String usage = "Usage: protein_ref.fa query.fa outfile word_size knn\n" + " This program takes a nucleotide or protein query sequence file, returns the top k best matching protein reference sequences based on amino acid kmer matching\n" + " word_size 4 is recommended for the best performance. Range from 3 to 6 is recommended.\n" + " protein_ref.fa must be protein sequences\n" + " query.fa can be either protein sequences or nucleotide sequences"; if ( args.length != 5){ System.err.println(usage); System.exit(1); } PrintStream out = new PrintStream(new File(args[2])); int wordSize = Integer.parseInt(args[3]); int k = Integer.parseInt(args[4]); ProteinSeqMatch theObj = new ProteinSeqMatch(args[0], wordSize); SequenceReader queryReader = new SequenceReader(new File(args[1]) ); Sequence seq; while ( ( seq = queryReader.readNextSequence()) != null){ ArrayList results = theObj.findTopKMatch(seq, k); for ( BestMatch m: results){ out.println(seq.getSeqName() + "\t" + m.getBestMatch().getSeqName() + "\t" + m.getSab() + "\t" + m.getBestMatch().getDesc()); } } queryReader.close(); out.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/000077500000000000000000000000001247756524500237005ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/GoodWordIterator.java000066400000000000000000000166771247756524500300220ustar00rootroot00000000000000 package edu.msu.cme.rdp.readseq.utils.orientation; import java.io.IOException; import java.io.StringReader; import java.util.NoSuchElementException; import java.util.Random; public class GoodWordIterator { private int curIndex = 0; private int numOfWords = 0; private int[] wordIndexArr; public static final int DEFAULT_WORDSIZE = 8; public static final int RNA_BASES = 4; //The number of rna bases (ATGC). Initially set to 4. private static int WORDSIZE = DEFAULT_WORDSIZE; // the size of a word private static boolean wordsizeHasSet = false; public static final float PERCENT_SELECTION = 0.125f; private static int MASK = (1 << (WORDSIZE * 2)) - 1; static final int MAX_ASCII = 128; private static int[] charIntegerLookup = new int[MAX_ASCII]; private final static int[] intComplementLookup = new int[RNA_BASES]; static { // initialize the integer complement look up table intComplementLookup[0] = 1; intComplementLookup[1] = 0; intComplementLookup[2] = 3; intComplementLookup[3] = 2; // initialize the char to integer mapping table for (int i = 0; i < MAX_ASCII; i++) { charIntegerLookup[i] = -1; } charIntegerLookup['A'] = 0; charIntegerLookup['U'] = 1; charIntegerLookup['T'] = 1; charIntegerLookup['G'] = 2; charIntegerLookup['C'] = 3; charIntegerLookup['a'] = 0; charIntegerLookup['u'] = 1; charIntegerLookup['t'] = 1; charIntegerLookup['g'] = 2; charIntegerLookup['c'] = 3; } /** * This is for testing purpose, for production use, recommend default size 8 * @param w */ public static void setWordSize(int w){ if ( wordsizeHasSet) { // this is to make sure the word size is only set once and remains the same for the process throw new IllegalStateException("word size has been set, can not set again"); } WORDSIZE = w; MASK = (1 << (WORDSIZE * 2)) - 1; wordsizeHasSet = true; } /** Creates a new instance of GoodWordIterator */ public GoodWordIterator(String seq) throws IOException { if ( !wordsizeHasSet) { // this is to make sure the word size is only set once and remains the same for the process setWordSize(WORDSIZE); } wordIndexArr = new int[seq.length()]; createWordIndex(seq); } public GoodWordIterator(String seq, int wordsLimit) throws IOException { if ( !wordsizeHasSet) { // this is to make sure the word size is only set once and remains the same for the process setWordSize(WORDSIZE); } wordIndexArr = new int[seq.length()]; createWordIndex(seq, wordsLimit); } /** Returns true if the iteration has more good element on deck. */ public boolean hasNext() { if (curIndex < numOfWords) { return true; } else { return false; } } /** Returns the next good element in the iteration. */ public int next() throws NoSuchElementException { int tmp; if (hasNext()) { tmp = curIndex; curIndex++; return wordIndexArr[tmp]; } else { throw new NoSuchElementException(); } } /** Fetchs every overlapping word, change to integer and save in an array */ private void createWordIndex(String seq) throws IOException { StringReader in = new StringReader(seq); int count = 0; int wordIndex = 0; int charIndex = 0; int c; while ((c = in.read()) != -1) { charIndex = charIntegerLookup[c]; if (charIndex == -1) { wordIndex = 0; count = 0; } else { count++; wordIndex <<= 2; wordIndex = wordIndex & (MASK); wordIndex = wordIndex | charIndex; if (count == WORDSIZE) { wordIndexArr[numOfWords] = wordIndex; numOfWords++; count--; } } } in.close(); } /** Fetchs a certain number of overlapping word, change to integer and save in an array * this is for partial sequence testing only */ private void createWordIndex(String seq, int wordsLimit) throws IOException { StringReader in = new StringReader(seq); int count = 0; int wordIndex = 0; int charIndex = 0; int c; while ((c = in.read()) != -1) { if (numOfWords >= wordsLimit) { break; } charIndex = charIntegerLookup[c]; if (charIndex == -1) { wordIndex = 0; count = 0; } else { count++; wordIndex <<= 2; wordIndex = wordIndex & (MASK); wordIndex = wordIndex | charIndex; if (count == WORDSIZE) { wordIndexArr[numOfWords] = wordIndex; numOfWords++; count--; } } } in.close(); } public static int getWordsize() { if ( !wordsizeHasSet) { // this is to make sure the word size is only set once and remains the same for the process setWordSize(WORDSIZE); } return WORDSIZE; } public static boolean isWordsizeHasSet(){ return wordsizeHasSet; } public int getMask() { return MASK; } public int getNumofWords() { return numOfWords; } public void resetCurIndex() { curIndex = 0; } public static int getCharIndex(int c) { return charIntegerLookup[c]; } public int[] getWordArr(){ if (this.getNumofWords() == 0) { throw new IllegalStateException("Error: The sequence contains 0 valid words"); } int[] wordList = new int[this.getNumofWords()]; this.resetCurIndex(); int num = 0; while (this.hasNext()) { wordList[num++] = this.next(); } return wordList; } public static int[] getRdmWordArr(int[] wordList, int min_bootstrap_words , Random randomGenerator) { // choose at one-eighth of the words or the min_bootstrap_words int numOfSelection = Math.max((int) (wordList.length * PERCENT_SELECTION), min_bootstrap_words); int[] testWordList = new int[numOfSelection]; for (int i = 0; i < numOfSelection; i++) { int randomIndex = randomGenerator.nextInt(wordList.length); testWordList[i] = wordList[randomIndex]; } return testWordList; } /** * Returns the reverse complement of the word in an integer array format. */ public static int[] getReversedWord(int[] word) { int length = word.length; int[] reverseWord = new int[length]; for (int w = 0; w < length; w++) { reverseWord[length - 1 - w] = intComplementLookup[ word[w]]; } return reverseWord; } /** * Returns an integer representation of a single word. */ public static int getWordIndex(int[] word) { int wordIndex = 0; for (int w = 0; w < word.length; w++) { wordIndex <<= 2; wordIndex = wordIndex & (MASK); wordIndex = wordIndex | word[w]; } return wordIndex; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/LogWordPriorFileParser.java000066400000000000000000000027501247756524500311150ustar00rootroot00000000000000// Decompiled by Jad v1.5.8g. Copyright 2001 Pavel Kouznetsov. // Jad home page: http://www.kpdus.com/jad.html // Decompiler options: packimports(3) // Source File Name: LogWordPriorFileParser.java package edu.msu.cme.rdp.readseq.utils.orientation; import java.io.*; import java.util.StringTokenizer; // Referenced classes of package edu.msu.cme.rdp.reverseengine: // TrainingDataException class LogWordPriorFileParser { LogWordPriorFileParser() { } void createLogWordPriorArr(Reader r, float arr[]) throws IOException, TrainingDataException { BufferedReader reader = new BufferedReader(r); String line = reader.readLine(); do { if((line = reader.readLine()) == null) break; StringTokenizer st = new StringTokenizer(line, "\t"); if(st.countTokens() != 2) throw new TrainingDataException("\nError: " + line + " does not have exact two numbers"); try { int wordIndex = Integer.parseInt(st.nextToken()); float logWordPrior = Float.parseFloat(st.nextToken()); arr[wordIndex] = logWordPrior; } catch(NumberFormatException e) { reader.close(); throw new TrainingDataException("\nError: The value for wordIndex or word prior is not a number at line : " + line); } } while(true); reader.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/OrientationChecker.java000066400000000000000000000025041247756524500303240ustar00rootroot00000000000000// Decompiled by Jad v1.5.8g. Copyright 2001 Pavel Kouznetsov. // Jad home page: http://www.kpdus.com/jad.html // Decompiler options: packimports(3) // Source File Name: OrientationChecker.java package edu.msu.cme.rdp.readseq.utils.orientation; // Referenced classes of package edu.msu.cme.rdp.reverseengine: // WordGenerator, TrainingInfo public class OrientationChecker { private OrientationChecker() { trainInfo = TrainingInfo.getInfo(); } public static OrientationChecker getChecker() { if (TrainingInfo.getDataFile() == null) { TrainingInfo.setDataFile(dataFile); } OrientationChecker checker = new OrientationChecker(); return checker; } public boolean isSeqReversed(String seqString) { WordGenerator generator = new WordGenerator(seqString); boolean reverse = false; float priorDiff; int wordIndex; for (priorDiff = 0.0F; generator.hasNext(); priorDiff += trainInfo.getWordPairPriorDiff(wordIndex)) { wordIndex = generator.next(); } if (priorDiff < 0.0F) { reverse = true; } return reverse; } TrainingInfo trainInfo; private static String dataFile = "/data/classifier/logWordPrior.txt"; public static void main(String[] args) { } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/ProteinWordGenerator.java000066400000000000000000000065721247756524500307000ustar00rootroot00000000000000/* * Copyright (C) 2014 wangqion * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.orientation; import edu.msu.cme.rdp.readseq.utils.ProteinUtils; import java.util.HashSet; /** * * @author wangqion */ public class ProteinWordGenerator { public static final int WORDSIZE = 4; private int wordSize = WORDSIZE; private ProteinUtils protUtils = ProteinUtils.getInstance(); public ProteinWordGenerator(int wordSize){ if ( wordSize < 3 || wordSize > 6){ // System.out.println("wordsize used: " + wordSize + ". Warning: recommended word size is " + WORDSIZE + ", or range [3-6]"); } this.wordSize = wordSize; } /** * returns all the overlapping words from a protein sequence * @param seq * @return */ public HashSet parseProtein(String seq){ HashSet wordSet = new HashSet(); for ( int i = 0; i <= seq.length() - wordSize; i++){ wordSet.add(seq.substring(i, i + wordSize).toLowerCase()); } return wordSet; } /** * This is recommended if frameshifts exist in the sequence. * This method translates a nucleotide sequence to protein in all three frames, * and returns the all the overlapping words from each frame. * @param nucl * @param translTable * @return */ public HashSet parseNuclAllFrames(String nucl){ return parseNuclAllFrames(nucl, 11); } public HashSet parseNuclAllFrames(String nucl, int translTable){ HashSet wordSet = new HashSet(); for ( int i = 0; i < 3; i++){ String s = protUtils.translateToProtein(nucl.substring(i ), true, translTable); HashSet tempSet = parseProtein(s); wordSet.addAll(tempSet); } return wordSet; } /** * This method translates a nucleotide sequence to protein assuming nucl sequence is in frame, * and returns the all the overlapping words * @param nucl * @param translTable * @return */ public HashSet parseNuclOneFrame(String nucl){ return parseNuclOneFrame(nucl, 11); } public HashSet parseNuclOneFrame(String nucl, int translTable){ return parseProtein(protUtils.translateToProtein(nucl, true, translTable)); } public static void main (String[] args) { ProteinWordGenerator theObj = new ProteinWordGenerator(ProteinWordGenerator.WORDSIZE); String nucl = "ttgaaacagattgcattttacggaaaaggagggattggaaagtcaactac"; HashSet wordSet = theObj.parseNuclAllFrames(nucl); for( String w: wordSet){ System.out.println(w); } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/TrainingDataException.java000066400000000000000000000010221247756524500307620ustar00rootroot00000000000000// Decompiled by Jad v1.5.8g. Copyright 2001 Pavel Kouznetsov. // Jad home page: http://www.kpdus.com/jad.html // Decompiler options: packimports(3) // Source File Name: TrainingDataException.java package edu.msu.cme.rdp.readseq.utils.orientation; public class TrainingDataException extends Exception { public TrainingDataException() { } public TrainingDataException(String msg) { super(msg); } public TrainingDataException(Throwable rootCause) { super(rootCause); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/TrainingInfo.java000066400000000000000000000074521247756524500271420ustar00rootroot00000000000000// Decompiled by Jad v1.5.8g. Copyright 2001 Pavel Kouznetsov. // Jad home page: http://www.kpdus.com/jad.html // Decompiler options: packimports(3) // Source File Name: TrainingInfo.java package edu.msu.cme.rdp.readseq.utils.orientation; import java.io.*; // Referenced classes of package edu.msu.cme.rdp.reverseengine: // TrainingDataException, LogWordPriorFileParser public class TrainingInfo { private TrainingInfo() { wordPairPriorDiffArr = new float[NUM_OF_WORDS]; try { java.net.URL aurl = getClass().getResource(dataFile); java.io.InputStream inStream = getClass().getResourceAsStream(dataFile); InputStreamReader in = new InputStreamReader(inStream); createLogWordPriorArr(in); } catch(IOException ex) { throw new RuntimeException(ex); } catch(TrainingDataException ex) { throw new RuntimeException(ex); } } public static void setDataFile(String file) { dataFile = file; } public static String getDataFile() { return dataFile; } public static synchronized TrainingInfo getInfo() { if(theInfo == null) { if(dataFile == null) throw new IllegalStateException("Must set the data file for TrainingInfo"); theInfo = new TrainingInfo(); } return theInfo; } private void createLogWordPriorArr(Reader reader) throws IOException, TrainingDataException { LogWordPriorFileParser parser = new LogWordPriorFileParser(); float logWordPriorArr[] = new float[NUM_OF_WORDS]; parser.createLogWordPriorArr(reader, logWordPriorArr); int origWord[] = new int[8]; generateWordPairDiffArr(logWordPriorArr, origWord, 0); } void generateWordPairDiffArr(float logWordPriorArr[], int word[], int beginIndex) { if(beginIndex < 0 || beginIndex > word.length) return; int origWordIndex = getWordIndex(word); int revWordIndex = getWordIndex(getReversedWord(word)); float origWordPrior = logWordPriorArr[origWordIndex]; float revWordPrior = logWordPriorArr[revWordIndex]; wordPairPriorDiffArr[origWordIndex] = origWordPrior - revWordPrior; for(int i = beginIndex; i < word.length; i++) { int origBase = word[i]; for(int j = 0; j < 4; j++) if(word[i] != j) { word[i] = j; generateWordPairDiffArr(logWordPriorArr, word, i + 1); word[i] = origBase; } } } private static int getWordIndex(int word[]) { int wordIndex = 0; for(int w = 0; w < word.length; w++) { wordIndex <<= 2; wordIndex &= 0xffff; wordIndex |= word[w]; } return wordIndex; } private static int[] getReversedWord(int word[]) { int length = word.length; int reverseWord[] = new int[length]; for(int w = 0; w < length; w++) reverseWord[length - 1 - w] = intComplementLookup[word[w]]; return reverseWord; } float getWordPairPriorDiff(int wordIndex) { return wordPairPriorDiffArr[wordIndex]; } private static int NUM_OF_WORDS = 0x10000; private static final int RNA_BASES = 4; private static int intComplementLookup[]; private float wordPairPriorDiffArr[]; public static TrainingInfo theInfo = null; private static String dataFile = null; static { intComplementLookup = new int[4]; intComplementLookup[0] = 1; intComplementLookup[1] = 0; intComplementLookup[2] = 3; intComplementLookup[3] = 2; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/utils/orientation/WordGenerator.java000066400000000000000000000040371247756524500273310ustar00rootroot00000000000000// Decompiled by Jad v1.5.8g. Copyright 2001 Pavel Kouznetsov. // Jad home page: http://www.kpdus.com/jad.html // Decompiler options: packimports(3) // Source File Name: WordGenerator.java package edu.msu.cme.rdp.readseq.utils.orientation; public class WordGenerator { public WordGenerator(String seq) { nextWord = 0; baseCount = 1; position = 0; invalid = false; seqString = seq; } public boolean hasNext() { int charIndex = 0; for(baseCount--; baseCount < 8 && position < seqString.length();) { char nextBase = seqString.charAt(position++); charIndex = charLookup[nextBase]; if(charIndex == -1) { baseCount = -1; charIndex = 0; } baseCount++; nextWord <<= 2; nextWord &= 0xffff; nextWord |= charIndex; } if(baseCount < 8) { invalid = true; return false; } else { return true; } } public int next() { if(invalid) throw new IllegalStateException("Attempt to call WordGenerator.next() when no more words."); else return nextWord; } public static final int WORD_SIZE = 8; public static final int MAX_NUM_WORD = 0x10000; public static final int MASK = 65535; private static final int MAX_ASCII = 128; private String seqString; private int nextWord; private int baseCount; private int position; private boolean invalid; private static int charLookup[]; static { charLookup = new int[128]; for(int i = 0; i < 128; i++) charLookup[i] = -1; charLookup[65] = 0; charLookup[84] = 1; charLookup[85] = 1; charLookup[71] = 2; charLookup[67] = 3; charLookup[97] = 0; charLookup[116] = 1; charLookup[117] = 1; charLookup[103] = 2; charLookup[99] = 3; } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/000077500000000000000000000000001247756524500217045ustar00rootroot00000000000000ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/FastaWriter.java000066400000000000000000000042751247756524500250120ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.writers; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.*; import java.io.File; import java.io.IOException; import java.io.OutputStream; import java.io.PrintStream; /** * * @author fishjord */ public class FastaWriter implements SequenceWriter { private PrintStream out; public FastaWriter(OutputStream is) { this(new PrintStream(is)); } public FastaWriter(String s) throws IOException { this(new File(s)); } public FastaWriter(File f) throws IOException { this(new PrintStream(f)); } public FastaWriter(PrintStream pw) { this.out = pw; } public void close() { out.close(); } public void writeSeq(Sequence s) { writeSeq(s.getSeqName(), s.getDesc(), s.getSeqString()); } public void writeSeq(String seqid, String desc, String seqString) { out.println(">" + seqid + " " + desc); out.println(seqString); } public void writeSeq(String seqid, String seqString) throws IOException { writeSeq(seqid, "", seqString); } public void writeRawQual(String seqid, byte[] qualSeq) { writeRawQual(seqid, "", qualSeq); } public void writeRawQual(String seqid, String desc, byte[] qualSeq) { StringBuilder qualString = new StringBuilder(); for(byte b : qualSeq) { qualString.append(b).append(" "); } writeSeq(seqid, desc, qualString.toString()); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/FastqWriter.java000066400000000000000000000061501247756524500250240ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.writers; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.core.FastqCore.QualityFunction; import java.io.File; import java.io.IOException; import java.io.OutputStream; import java.io.PrintStream; /** * * @author fishjord */ public class FastqWriter implements SequenceWriter { private PrintStream out; private QualityFunction qualFunction; private Byte defaultQuality; public FastqWriter(OutputStream is, QualityFunction qualFunction) { this(new PrintStream(is), qualFunction); } public FastqWriter(String s, QualityFunction qualFunction) throws IOException { this(new File(s), qualFunction); } public FastqWriter(File f, QualityFunction qualFunction) throws IOException { this(new PrintStream(f), qualFunction); } public FastqWriter(File f, QualityFunction qualFunction, byte defaultQual) throws IOException { this(new PrintStream(f), qualFunction, defaultQual); } public FastqWriter(PrintStream pw, QualityFunction qualFunction) { this.out = pw; this.qualFunction = qualFunction; } public FastqWriter(PrintStream pw, QualityFunction qualFunction, byte defaultQual) { this(pw, qualFunction); defaultQuality = defaultQual; } public void close() { out.close(); } public void writeSeq(Sequence seq) throws IOException { if(seq.getClass() == QSequence.class) { QSequence s = (QSequence)seq; writeSeq(s.getSeqName(), s.getDesc(), s.getSeqString(), s.getQuality()); } else if(defaultQuality != null) { byte[] qual = new byte[seq.getSeqString().length()]; for(int index = 0;index < qual.length;index++) { qual[index] = defaultQuality; } writeSeq(seq.getSeqName(), seq.getDesc(), seq.getSeqString(), qual); } else { throw new IOException("Fastq writer can only write QSequences"); } } public void writeSeq(String seqid, String desc, String seqString, byte[] qualSeq) { out.println("@" + seqid + " " + desc); out.println(seqString); out.println("+"); StringBuffer qual = new StringBuffer(); for(byte b : qualSeq) { qual.append(qualFunction.translate(b)); } out.println(qual); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/PhylipWriter.java000066400000000000000000000046471247756524500252240ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.writers; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.io.IOException; import java.io.OutputStream; import java.io.PrintStream; import java.util.List; /** * * @author fishjord */ public class PhylipWriter implements SequenceWriter { private PrintStream out; private int seqLength; private static final int TAX_ID_LENGTH = 10; public PhylipWriter(OutputStream o, int numTaxa, int seqLength) { this.out = new PrintStream(o); out.println(numTaxa + " " + seqLength); this.seqLength = seqLength; } private static String getSeqId(String seqid) { for(int index = seqid.length();index < TAX_ID_LENGTH;index++) seqid += " "; return seqid; } public void writeSeq(Sequence seq) throws IOException { writeSeq(seq.getSeqName(), seq.getSeqString()); } public void writeSeq(String seqid, String seqString) throws IOException { if(seqString.length() != seqLength) throw new IOException("Sequencec seq " + seqid + " is not the expected length (" + seqLength + ")"); out.println(getSeqId(seqid) + seqString); } public void writeSeq(String seqid, String desc, String seqString) throws IOException { throw new UnsupportedOperationException("Phylip format doesn't support sequence descriptions"); } public void close() throws IOException { out.close(); } public static void writeSequences(List seqs, OutputStream out) throws IOException { PhylipWriter writer = new PhylipWriter(out, seqs.size(), seqs.get(0).getSeqString().length()); for(Sequence seq : seqs) writer.writeSeq(seq); out.close(); } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/SFFWriter.java000066400000000000000000000137331247756524500243710ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.writers; import edu.msu.cme.rdp.readseq.readers.core.SFFCore; import edu.msu.cme.rdp.readseq.readers.core.SFFCore.CommonHeader; import edu.msu.cme.rdp.readseq.readers.core.SFFCore.ReadBlock; import java.io.File; import java.io.IOException; import java.io.RandomAccessFile; import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.List; import java.util.Map; /** * * @author fishjord */ public class SFFWriter { private RandomAccessFile out; private Map seqIndex = new HashMap(); private String manifest; public SFFWriter(File outFile, CommonHeader ch) throws IOException { if(outFile.exists()) { if(!outFile.delete()) { throw new IOException(outFile + " exists and could not be deleted"); } } out = new RandomAccessFile(outFile, "rw"); writeCommonHeader(ch); } public SFFWriter(File outFile, CommonHeader ch, String manifest) throws IOException { this(outFile, ch); this.manifest = manifest; } public void close() throws IOException { //We should already be at the end of the file, if not something bad happened... long indexStart = out.getFilePointer(); if(manifest != null) { out.writeInt(SFFCore.mftMagicNumber); out.writeInt(SFFCore.v1MagicNumber); out.writeInt(manifest.getBytes().length); out.writeInt(Integer.MIN_VALUE); out.write(manifest.getBytes()); } else { out.writeInt(SFFCore.srtMagicNumber); out.writeInt(SFFCore.v1MagicNumber); out.writeInt(0); } List seqids = new ArrayList(seqIndex.keySet()); Collections.sort(seqids); //Put the SORT in sorted index for(String seqid : seqids) { out.write(seqid.getBytes()); long offset = seqIndex.get(seqid); //Don't look TOO close, the basic thing is we need to pack 5 bytes of a long and 0xff in to the file //Also 0xff has a special meaning so it can't appear in the long (max val = 255, not 256 basically) long pt4 = 0; //Roche never seems to use the 5th byte of this long so neither will we long pt3 = offset; long pt0 = pt3 % 255; pt3 -= pt0; long pt1 = pt3 % 65025; pt3 -= pt1; long pt2 = pt3 % 16581375; pt3 -= pt2; pt3 /= 16581375; pt2 /= 65025; pt1 /= 255; byte[] indexBytes = new byte[] { (byte)(pt4 & 0xff), (byte)(pt3 & 0xff), (byte)(pt2 & 0xff), (byte)(pt1 & 0xff), (byte)(pt0 & 0xff), (byte)0xff }; // Pack it! out.write(indexBytes); } int indexSize = (int)(out.getFilePointer() - indexStart); alignToBoundary(); if(manifest != null) { out.seek(indexStart + 12); //Seek back to where the data size is suppose to be int dataSize = indexSize - 16 - manifest.getBytes().length; //Size of just the index (no manifest, no magic numbers) out.writeInt(dataSize); } out.seek(8); //Jump back to write out the index offset, length, and read count out.writeLong(indexStart); //Index offset out.writeInt(indexSize); //index size out.writeInt(seqids.size()); //Number of reads out.close(); } private void writeCommonHeader(CommonHeader ch) throws IOException { out.writeInt(ch.getMagicNumber()); out.writeInt(ch.getVersion()); out.writeLong(Long.MIN_VALUE); //index offset(written on close) out.writeInt(Integer.MIN_VALUE); //index length (written on close) out.writeInt(Integer.MIN_VALUE); //num reads (written on close) out.writeShort(ch.getHeaderLength()); out.writeShort(ch.getKeyLength()); out.writeShort(ch.getFlowLength()); out.writeByte(ch.getFlowgramFormat()); out.write(ch.getFlow().getBytes()); out.write(ch.getKey().getBytes()); alignToBoundary(); } public void writeReadBlock(ReadBlock rb) throws IOException { seqIndex.put(rb.getName(), out.getFilePointer()); out.writeShort(rb.getHeaderLength()); out.writeShort(rb.getNameLength()); out.writeInt(rb.getNumBases()); out.writeShort(rb.getClipQualLeft()); out.writeShort(rb.getClipQualRight()); out.writeShort(rb.getClipAdapterLeft()); out.writeShort(rb.getClipAdapterRight()); out.write(rb.getName().getBytes()); for(int index = 0;index < rb.getFlowgrams().length;index++) { out.writeShort(rb.getFlowgrams()[index]); } out.write(rb.getFlowIndex()); out.write(rb.getSeq().getBytes()); out.write(rb.getQual()); alignToBoundary(); } private void alignToBoundary() throws IOException { long pos = out.getFilePointer(); if (pos % 8 != 0) { byte[] padding = new byte[(int)(8 - pos % 8)]; //There is something seriously wrong if THIS can't be stored in an int... out.write(padding); //Thank you java for zeroing all new variables } } } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/SequenceWriter.java000066400000000000000000000017551247756524500255240ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.writers; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.io.IOException; /** * * @author fishjord */ public interface SequenceWriter { public void writeSeq(Sequence seq) throws IOException; public void close() throws IOException; } ReadSeq-2.0.2/src/edu/msu/cme/rdp/readseq/writers/StkWriter.java000066400000000000000000000150741247756524500245140ustar00rootroot00000000000000/* * Copyright (C) 2012 wangqion * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.writers; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import java.io.File; import java.io.IOException; import java.io.OutputStream; import java.io.PrintStream; import java.util.ArrayList; import java.util.List; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.commons.cli.PosixParser; /** * * @author wangqion */ public class StkWriter implements SequenceWriter { public static final String STK_HEADER = "# STOCKHOLM 1.0"; private PrintStream out; private int max_seqIDLength = 0; private static final int GAP_LENGTH = 10; public StkWriter(int seqIDLength, OutputStream o) throws IOException { this(seqIDLength, o, STK_HEADER); } public StkWriter(int seqIDLength, OutputStream o, String header) throws IOException { this.out = new PrintStream(o); max_seqIDLength = seqIDLength; out.println(header + "\n"); } public StkWriter(SequenceReader reader, OutputStream o, String header) throws IOException { this(getSeqIDLength(reader), o, header); } public static int getSeqIDLength(SequenceReader reader) throws IOException{ int seqIDLength = 0; int seqLength = 0; Sequence seq; while ( (seq = reader.readNextSequence()) != null) { if ( seq.getSeqName().trim().length() > seqIDLength){ seqIDLength = seq.getSeqName().trim().length(); } if (seqLength == 0){ seqLength = seq.getSeqString().trim().length(); }else if ( seq.getSeqString().trim().length() != seqLength){ throw new IOException("Sequencec seq " + seq.getSeqName() + " is not the expected length (" + seqLength + ")"); } } reader.close(); return seqIDLength; } public static int getSeqIDLength(List seqs) throws IOException{ int seqIDLength = 0; int seqLength = 0; for ( Sequence seq: seqs) { if ( seq.getSeqName().trim().length() > seqIDLength){ seqIDLength = seq.getSeqName().trim().length(); } if (seqLength == 0){ seqLength = seq.getSeqString().trim().length(); }else if ( seq.getSeqString().trim().length() != seqLength){ throw new IOException("Sequencec seq " + seq.getSeqName() + " is not the expected length (" + seqLength + ")"); } } return seqIDLength; } /** * need to pad spaces * @param seqid * @return */ private String getSeqId(String seqid) { return String.format("%1$-" + (max_seqIDLength + GAP_LENGTH) + "s", seqid); } public void writeSeq(Sequence seq) throws IOException { writeSeq(seq.getSeqName(), seq.getSeqString()); } public void writeSeq(String seqid, String seqString) throws IOException { out.println(getSeqId(seqid) + seqString); } public void writeSeq(String seqid, String desc, String seqString) throws IOException { throw new UnsupportedOperationException("Phylip format doesn't support sequence descriptions"); } public void writeEndOfBlock() throws IOException{ out.println("//"); } public void close() throws IOException { out.close(); } public static void writeSequences(SequenceReader reader, OutputStream out) throws IOException { writeSequences(reader, out, STK_HEADER); } public static void writeSequences(SequenceReader reader, OutputStream out, String header) throws IOException { ArrayList seqList = new ArrayList(); Sequence seq; while ( (seq = reader.readNextSequence()) != null) { seqList.add(seq); } reader.close(); StkWriter writer = new StkWriter(getSeqIDLength(seqList), out, header); for(Sequence aseq : seqList) writer.writeSeq(aseq); writer.writeEndOfBlock(); writer.close(); } public static void main(String[] args) throws Exception{ Options options = new Options(); options.addOption("r", "removeref", false, "is set, do not write the GC reference sequences to output"); options.addOption("h", "header", true, "the header of the output file in case a differenet stk version, default is " + STK_HEADER); String header = STK_HEADER; boolean removeRef = false; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("removeref")) { removeRef = true; } if (line.hasOption("header")) { header = line.getOptionValue("header"); } args = line.getArgs(); if ( args.length < 2){ throw new Exception("Need input and output files"); } } catch (Exception e) { new HelpFormatter().printHelp("USAGE: to-stk ", options); System.err.println("ERROR: " + e.getMessage()); System.exit(1); return; } SequenceReader reader = new SequenceReader(new File(args[0])); PrintStream out = new PrintStream(new File(args[1])); StkWriter writer = new StkWriter(reader, out, header); reader = new SequenceReader(new File(args[0])); Sequence seq; while ( (seq = reader.readNextSequence()) != null) { if ( seq.getSeqName().startsWith("#") && removeRef){ continue; } writer.writeSeq(seq); } writer.writeEndOfBlock(); writer.close(); reader.close(); } } ReadSeq-2.0.2/test/000077500000000000000000000000001247756524500140375ustar00rootroot00000000000000ReadSeq-2.0.2/test/454Reads.sff000066400000000000000000000233301247756524500160330ustar00rootroot00000000000000.sff$0H TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTCAG wGF040U105F9RVGggccrhnnhhiei` dphRrTxXZXV!\Y a t ^d nf^ d gfa  xkr h _b #jd i fn`e Y ]i id gc e gigi ddlg  d l cf^_ a f fh` nch fmdft a # m\a! c_`dplcxfb U m a tfq e],^ ` lf_ ied de]Z ~`f]i` g f hV~Z`S e f ^m k *chv[ Xd_ ke ree` s(8 Vh_e rl a ehd f eeYp  + c N[ ioJ jk[ r ] Xa pZe bfY vk d ^qgc fU eeb  dT Sel`                 TCAGACGAGTGCGTTGCGACCCGAAGGCCGACTCCACCCGCCTGATTCTGAACAGCAAAGCTCAAACCACGGTTATGGACCTGGCCCGTGAACGGGGAACGGTGGAGGATCTGGAACTGGAAGATGTGTCGGTGGAAGGTCATCTGGGGGTGCGCTGTGCGGAGTCCGGCGGCCCGGAACCGGGTGTGGGCTGTGCCGGACGGGGTGTGATCACCGCCATTTAACTTTCTTGAGGAAAACGGTGCTTACACCGAGGATACAGATTATGTCTTCTATGATGTTCTGGGTGATGTAGTCTGCGGGGGATTTGCCATGCCGATCCGTGAGAACAAAGCCAAGGAAATCTATATCGTCACCTCCGGCGAGATGATGGCCATCTGAGCGGGCTGGCAAGGCGCATAGNN(((((((((((((((((((" !$$$$((((((((((((((''((((((((((((((((''%((((($& $(((((((&&&&((((((((((((((((((((((((((((((((((((((((((((((((((($$$%%$"$"((((&((!!&%(((((& $$!# (((((((((((((&"""(((((((((('"""" "((''&('''(((((((((&$$$$$(&&&&(((((((((!$$$$#$""((($$$((((($$&&&""""!!$($(($&#&$ ! vGF040U105FRBRWeh eemjqqdljnibcdiki  a ^ e cd d i;^ ^ cd e n cmodg2ec`_ ) dco_cj  e j fgdd gdf W a cg elnh!kYim[ d \ j f igl\  d \dl\kna \ofaxO 3(nT[?t_qf e d[rXY m ekqeq a k$_u eoo blp\ PfXW{dlVs^ l Ur`s ^Zy i v b ^ k f c 4n gh g ^\Zji k f g` e 9t l i ]f t ^ ho ` Oiq ;t  .Z f^eXr^bkn Ykof Z<jlsk g\ th q eM b'aeg Yi f] vZp                          TCAGACGAGTGCGTTGCGATCCGAAGGCTGACTCCACCCGCCTGATTCTGAACAGCAAAGCTCAAACCACGGTTATGGACCTGGCTCGTGAACGGGGAACGGTGGAGGATCTGGAACTGAAAGATGTGTTGGTGGAAGGTCATCTGGGGGTGCGCTGTGCGGAGTCCGGCGGCCCGGAACCGGGTGTGGGCTGTGCCGGACGGGGTGTGATCACCGCCATTAACTTTCTTGAGGAAAACGGTGCTTACACCGAGGATACAGATTATGTCTTCTATGATGTTCTGGGTGATGTAGTCTGCGGGGGATTTGCCATGCCGATCCGTGAGAACAAAGCCAAGGAAATCTATATCGTCACCTCCGGTGAAATGATGGCCATCTGAGCGGGCTGGCAAGGCGCATAGNN((((((((((((((((((((((((((((((((((((&&&((((((((((((((((('''(((('''((((((((((((((((((((((((((("" (((((((((((((((((((((('''((((((((((((((((((((('$(((((((((((((''''''$$$##''""!!!(#''(((((((((('%(((((('''''(((((('''' #(((!!((((('""#'(((((''''((((((''''(((('''''((((((('''(((((((((((((('''(((((((((((((((((('''"&"((((((('''((((((((((##""'(((((("""(((((((((((((((('''(((((((((((((''' wGF040U105FT65Leak^ohmodficgdefhb$  e diff cj'e b af`e ef mhe gdi f dfgehed i i e b` gf fegfd gegi e gih  _ afd cghhef gc ie _iif `f hjff edlhlj i dfk _j +h]] +d ged iblg k r ^^b bjm g bg edq g jm f bjj c N_wqh  nf\ c|Y ]WUZPclYv oiVrYeetq~ [Zk]Wvi g:]p f;  ]0 ia}f(cbqWw g  ~ J$ a c RbmStl W_egxj h YXu!{  b,fR[g_WcmbTg] n k v  \o ga yVk                         TCAGACGAGTGCGTTGCGATCCCAAGGCTGACTCCACCCGCCTGATCCTGCACGCCAAGGCGCAGACGACGGTCATGGACCTGGTGCGCGAGCTCGGCACCGTGGAGGACCTGGAATTGGAAGACGTCATGAAGGTCGGCTACGGCGACGTGAAGTGCGTTGAGTCCGGCGGTCCCGAGCCGGGTGTCGGCTGTGCAGGCCGCGGCGTCATCACCGCCATCAACTTCCTCGAAGAGAACGGTGCCTACACCCCTGACCTCGACTTCGTCTTCTACGACGTTCTGGGCGACGTCGTTTGTCGGCGGTTTCGTCCATGCCGATCCGCGAGAACAAGGCCGAGGAGATCTACATCGTCTGCTCCGGTGAAATGATGGCGATCTGAGCGGGCTGGCAAGGCGCATAG(((((((((((((((((((('''((((((((((((('''(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((('''((((('''((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("""($$  $"# !$$$$$$((($$ #!&$$$((((((((((((((((((.mft1.00< 454 GF040U105 R_2010_04_22_17_47_08_FLX03070149_adminrig_Tiedje042210 D_2010_04_23_12_56_16_bioinfo-2_signalProcessingAmplicons /data/R_2010_04_22_17_47_08_FLX03070149_adminrig_Tiedje042210/D_2010_04_23_12_56_16_bioinfo-2_signalProcessingAmplicons/ 1.1.03 GF040U105F9RVGKGF040U105FRBRWvGF040U105FT65LReadSeq-2.0.2/test/BMC200_trimmed.fasta000066400000000000000000000020701247756524500174220ustar00rootroot00000000000000>GB4XUSJ08J0EJJ length=331 GGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCGCGCCCTAAACGATGTCAATTAGCTGTTGGGCAACCTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAA >GB4XUSJ08JZGI6 length=333 CTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGCTTAGATACCCTGGTAGTCCACGCTGTAAACGGTGGGTACTAGGTGTGGGGTCCACTCCACGGGTTCCGTGCCGTAGCTAACGCTTTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAA >GB4XUSJ08JUMTI length=329 CGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGAGTGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGTGCGAAAGTGTGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACACCCTAAACGATGTACGTTGGCTAAGCGCAGGATGCTGCGCTTGGCGAAGCTAACGCGATAAACGTACCGCCTGGGAAGTACGGCCGCAAGGTTGAA ReadSeq-2.0.2/test/BMC200_trimmed.qual000066400000000000000000000057721247756524500173020ustar00rootroot00000000000000>GB4XUSJ08J0EJJ length=331 21 21 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 34 34 33 33 39 39 39 40 40 40 40 40 39 39 39 30 30 30 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 21 21 35 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 39 39 39 40 40 40 40 39 39 39 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 34 34 34 40 40 40 40 40 40 40 40 40 39 28 28 28 28 35 29 40 40 40 40 40 40 40 40 40 39 39 36 36 38 38 22 22 24 >GB4XUSJ08JZGI6 length=333 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 32 32 32 40 40 40 40 40 39 39 39 40 40 40 36 26 24 24 26 17 17 15 15 23 28 25 25 23 25 23 20 22 24 24 25 36 40 40 40 38 38 33 33 33 33 36 36 36 26 17 17 17 17 24 23 36 36 40 36 36 36 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 40 40 40 40 40 40 40 40 40 39 39 39 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 33 33 34 33 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 30 30 35 39 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 32 32 34 34 40 39 39 39 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 37 40 40 40 40 36 20 19 19 19 34 24 26 34 26 26 26 26 30 29 40 40 40 40 40 40 40 40 40 30 30 30 30 40 40 32 32 32 >GB4XUSJ08JUMTI length=329 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 40 40 40 39 39 30 30 29 29 35 34 36 40 30 33 34 27 27 27 24 27 30 32 36 36 34 29 24 20 22 22 23 25 30 19 30 26 28 30 33 36 36 40 40 40 40 40 40 40 40 40 39 39 39 40 40 38 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 26 26 26 26 30 30 34 34 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 34 34 35 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 38 40 40 40 40 34 34 34 34 40 40 40 38 38 38 40 40 40 33 20 22 22 22 28 31 28 22 17 15 17 22 22 31 36 36 30 36 36 39 40 40 40 39 39 39 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 30 30 30 30 40 40 40 40 40 40 40 40 39 39 34 34 34 40 40 40 40 40 40 40 40 40 40 30 30 30 40 40 40 40 39 39 36 36 40 40 40 36 36 36 26 26 26 26 30 24 24 ReadSeq-2.0.2/test/edu/000077500000000000000000000000001247756524500146145ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/000077500000000000000000000000001247756524500154205ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/000077500000000000000000000000001247756524500161645ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/000077500000000000000000000000001247756524500167515ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/000077500000000000000000000000001247756524500203755ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/IndexedSeqReaderTest.java000066400000000000000000000063421247756524500252610ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import java.io.File; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class IndexedSeqReaderTest { /** * Test of getSeqIds method, of class IndexedSeqReader. */ @Test public void testGetSeqIds() throws Exception { IndexedSeqReader reader = new IndexedSeqReader(new File("test/test.fa")); Sequence s = reader.readSeq("test1"); assertEquals("test1", s.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~", s.getSeqString()); s = reader.readSeq("struct"); assertEquals("struct", s.getSeqName()); assertEquals(".-<({[])}>-.", s.getSeqString()); reader.close(); reader = new IndexedSeqReader(new File("test/test.fa"), true); s = reader.readSeq("test1"); assertEquals("test1", s.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN", s.getSeqString()); s = reader.readSeq("test2"); assertEquals("test2", s.getSeqName()); assertEquals("ccccccccccccccccccccccccccccccccccccc", s.getSeqString()); reader.close(); } /** * Test of readSeq method, of class IndexedSeqReader. */ @Test public void testReadSeq() throws Exception { IndexedSeqReader reader = new IndexedSeqReader(new File("test/test.fa")); assertEquals("test0", reader.getSeqIds().get(0)); assertEquals("test1", reader.getSeqIds().get(1)); assertEquals("test2", reader.getSeqIds().get(2)); reader.close(); } @Test public void testExternalIndex() throws Exception { IndexedSeqReader.indexSeqFile(new File("test/test.fa"), new File("test/test.index"), SequenceFormat.FASTA); IndexedSeqReader reader = new IndexedSeqReader(new File("test/test.fa"), new File("test/test.index")); Sequence s = reader.readSeq("test1"); assertEquals("test1", s.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~", s.getSeqString()); reader.close(); } @Test public void testMaskingReader() throws Exception { IndexedSeqReader reader = new IndexedSeqReader(new File("test/test.fa"), "mask"); Sequence s = reader.readSeq("test1"); assertEquals("test1", s.getSeqName()); assertEquals("KX", s.getSeqString()); reader.close(); } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/SequenceParserTest.java000066400000000000000000000062241247756524500250310ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.readers.SequenceReader; import java.io.FileInputStream; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class SequenceParserTest { /** * Test of getNextSequence method, of class SequenceReader. */ @Test public void testGetNextSequence() throws Exception { SequenceReader parser = new SequenceReader(new FileInputStream("test/test.fa")); Sequence seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("test0", seq.getSeqName()); assertEquals("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", seq.getSeqString()); seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("test1", seq.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~", seq.getSeqString()); seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("test2", seq.getSeqName()); assertEquals("ccccccccccccccccccccccccccccccccccccc", seq.getSeqString()); seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("struct", seq.getSeqName()); assertEquals(".-<({[])}>-.", seq.getSeqString()); seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("mask", seq.getSeqName()); assertEquals("00000................1000000000A00000", seq.getSeqString()); assertNull(parser.readNextSequence()); parser.close(); } /** * Test of getNextSequence method, of class SequenceReader. */ @Test public void testWhitespace() throws Exception { SequenceReader parser = new SequenceReader(new FileInputStream("test/test_1.fa")); Sequence seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("test0", seq.getSeqName()); assertEquals("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", seq.getSeqString()); seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("test1", seq.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~", seq.getSeqString()); seq = parser.readNextSequence(); assertNotNull(seq); assertEquals("test2", seq.getSeqName()); assertEquals("ccccccccccccccccccccccccccccccccccccc", seq.getSeqString()); parser.close(); } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/readers/000077500000000000000000000000001247756524500220225ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/readers/QSeqReaderTest.java000066400000000000000000000071521247756524500255260ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import edu.msu.cme.rdp.readseq.QSequence; import java.io.File; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class QSeqReaderTest { private static final String expectedSeqName = "GB4XUSJ08J0EJJ"; private static final String expectedSeq = "GGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCGCGCCCTAAACGATGTCAATTAGCTGTTGGGCAACCTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAA"; private static final byte[] expectedQual = new byte[]{21, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 34, 34, 33, 33, 39, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 30, 30, 30, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 21, 35, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 39, 39, 39, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 34, 34, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 28, 28, 28, 28, 35, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 39, 39, 36, 36, 38, 38, 22, 22, 24}; public QSeqReaderTest() { } @Test public void testPairedFile() throws Exception { File seqFile = new File(QSeqReaderTest.class.getResource("/BMC200_trimmed.fasta").getFile()); File qualFile = new File(QSeqReaderTest.class.getResource("/BMC200_trimmed.qual").getFile()); QSeqReader seqReader = new QSeqReader(seqFile, qualFile); QSequence seq = (QSequence)seqReader.readNextSequence(); assertEquals("Sequence name doesn't match =(", expectedSeqName, seq.getSeqName()); assertEquals("Expected sequence doesn't match actual seq", expectedSeq, seq.getSeqString()); assertEquals("Quality sequence length doesn't match", expectedQual.length, seq.getQuality().length); for (int index = 0; index < expectedQual.length; index++) { assertEquals("Qual[" + index + "]", expectedQual[index], seq.getQuality()[index]); } } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/readers/SeqFileReaderTest.java000066400000000000000000000777021247756524500262150ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers; import java.io.BufferedReader; import java.io.FileReader; import java.io.BufferedInputStream; import java.io.ByteArrayInputStream; import edu.msu.cme.rdp.readseq.QSequence; import java.io.IOException; import java.io.File; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class SeqFileReaderTest { @Test public void testReadSTKFile() throws IOException { String exp1Id = "GF040U105F9RVG"; String exp1Seq = "TRLILNSKAQTTVMDLARERGTVEDLELEDVSVEGHLGVRCAESGGPEPGVGCAGRGVITAINFLEENGAYTEdTDYVFYDVLGDVVCGGFAMPIRENKAKEIYIVT"; String exp2Id = "GF040U105FRBRW"; String exp2Seq = "TRLILNSKAQTTVMDLARERGTVEDLELKDVLVEGHLGVRCAESGGPEPGVGCAGRGVITAINFLEENGAYTEdTDYVFYDVLGDVVCGGFAMPIRENKAKEIYIVT"; SequenceReader seqFileReader = new SequenceReader(new File("test/test.sto")); Sequence seq1 = seqFileReader.readNextSequence(); assertEquals(exp1Id, seq1.getSeqName()); assertEquals(exp1Seq, seq1.getSeqString()); seq1 = seqFileReader.readNextSequence(); assertEquals(exp2Id, seq1.getSeqName()); assertEquals(exp2Seq, seq1.getSeqString()); assertEquals("GF040U105FT65L", seqFileReader.readNextSequence().getSeqName()); assertEquals("#=GC PP_cons", seqFileReader.readNextSequence().getSeqName()); assertEquals("#=GC RF", seqFileReader.readNextSequence().getSeqName()); } @Test public void testReadSFFFile() throws IOException { String exp1Id = "GF040U105F9RVG"; String exp1Seq = "ACGAGTGCGTTGCGACCCGAAGGCCGACTCCACCCGCCTGATTCTGAACAGCAAAGCTCAAACCACGGTTATGGACCTGGCCCGTGAACGGGGAACGGTGGAGGATCTGGAACTGGAAGATGTGTCGGTGGAAGGTCATCTGGGGGTGCGCTGTGCGGAGTCCGGCGGCCCGGAACCGGGTGTGGGCTGTGCCGGACGGGGTGTGATCACCGCCATTTAACTTTCTTGAGGAAAACGGTGCTTACACCGAGGATACAGATTATGTCTTCTATGATGTTCTGGGTGATGTAGTCTGCGGGGGATTTGCCATGCCGATCCGTGAGAACAAAGCCAAGGAAATCTATATCGTCACCTCCGGCGAGATGATGGCC"; String exp2Id = "GF040U105FRBRW"; String exp2Seq = "ACGAGTGCGTTGCGATCCGAAGGCTGACTCCACCCGCCTGATTCTGAACAGCAAAGCTCAAACCACGGTTATGGACCTGGCTCGTGAACGGGGAACGGTGGAGGATCTGGAACTGAAAGATGTGTTGGTGGAAGGTCATCTGGGGGTGCGCTGTGCGGAGTCCGGCGGCCCGGAACCGGGTGTGGGCTGTGCCGGACGGGGTGTGATCACCGCCATTAACTTTCTTGAGGAAAACGGTGCTTACACCGAGGATACAGATTATGTCTTCTATGATGTTCTGGGTGATGTAGTCTGCGGGGGATTTGCCATGCCGATCCGTGAGAACAAAGCCAAGGAAATCTATATCGTCACCTCCGGTGAAATGATGGCC"; SequenceReader seqFileReader = new SequenceReader(new File("test/454Reads.sff")); Sequence seq1 = seqFileReader.readNextSequence(); assertEquals(exp1Id, seq1.getSeqName()); assertEquals(exp1Seq, seq1.getSeqString()); seq1 = seqFileReader.readNextSequence(); assertEquals(exp2Id, seq1.getSeqName()); assertEquals(exp2Seq, seq1.getSeqString()); } @Test public void testReadStream() throws IOException { String seqs = ">test1\nacgt\n>test2\ngggg"; String exp1Id = "test1"; String exp1Seq = "acgt"; String exp2Id = "test2"; String exp2Seq = "gggg"; SequenceReader seqFileReader = new SequenceReader(new BufferedInputStream(new ByteArrayInputStream(seqs.getBytes()))); Sequence seq1 = seqFileReader.readNextSequence(); assertEquals(exp1Id, seq1.getSeqName()); assertEquals(exp1Seq, seq1.getSeqString()); seq1 = seqFileReader.readNextSequence(); assertEquals(exp2Id, seq1.getSeqName()); assertEquals(exp2Seq, seq1.getSeqString()); } @Test public void testReadFastaFile() throws IOException { SequenceReader reader = new SequenceReader(new File("test/test.fa")); Sequence s = reader.readNextSequence(); assertEquals("test0", s.getSeqName()); assertEquals("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", s.getSeqString()); s = reader.readNextSequence(); assertEquals("test1", s.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~", s.getSeqString()); reader.close(); } @Test public void testReadFastqFile() throws IOException { String exp1Id = "001043_1783_0863"; String exp1Seq = "CTGATCATTGGGCGTAAAGAGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCGAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAAATACCCTCGTA"; String exp2Id = "001051_2436_2741"; String exp2Seq = "CATCTCACTGGGCATAAAGGGCACGCAGACGGACCGACAGGTCGTTTGTGAAAGGCGAGGGCTCAACCCTTGTTTGCGGACGAAACCGTCGGACTGGAGTACCGGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCCGGATACTGACGCTCAAGTGCGAAAGCTGGGGGAGCGAACGGGATTAGATACCCTTGTA"; SequenceReader seqFileReader = new SequenceReader(new File("test/test_init_v4.fastq")); Sequence seq1 = seqFileReader.readNextSequence(); assertTrue(seq1 instanceof QSequence); assertEquals(exp1Id, seq1.getSeqName()); assertEquals(exp1Seq, seq1.getSeqString()); seq1 = seqFileReader.readNextSequence(); assertEquals(exp2Id, seq1.getSeqName()); assertEquals(exp2Seq, seq1.getSeqString()); } @Test public void testReadEMBL() throws IOException { SequenceReader reader = new SequenceReader(new File("test/test.embl")); Sequence seq; String expectedSeqid; String expectedSeq; expectedSeqid = "FR838948"; expectedSeq = "atgaaaataatcaatattggaattcttgcccatgtagacgctggaaagacgaccttgacggagagcctgctatatgccagcggagccatttcagaaccggggagcgtcgaaaaagggacaacgaggacggacaccatgtttttggagcggcagcgtgggattaccattcaagcggcagtcacttccttccagtggcacagatgtaaagttaacattgtggatacgcccggccacatggattttttggcggaggtgtaccgctctttggctgttttagatggggccatcttggtgatctccgctaaagatggcgtgcaggcccagacccgtattctgttccatgccctgcggaaaatgaacattcccaccgttatctttatcaacaagatcgaccaggctggcgttgatttgcagagcgtggttcagtctgttcgggataagctctccgccgatattatcatcaagcagacggtgtcgctgtccccggaaatagtcctggaggaaaataccgacatagaagcatgggatgcggtcatcgaaaataacgatgaattattggaaaagtatatcgcaggagaaccaatcagccgggaaaaacttgcgcgggaggaacagcagcgggttcaagacgcctccctgttcccggtctatcatggcagcgccaaaaatggccttggcattcaaccgttgatggatgcggtgacagggctgttccaaccgattggggaacaggggggcgccgccctatgcggcagcgttttcaaggttgagtacaccgattgcggccagcggcgtgtctatctacggttatacagcggaacgctgcgcctgcgggatacggtggccctggccgggagagaaaagctgaaaatcacagagatgcgtattccatccaaaggggaaattgttcggacagacaccgcttatcagggtgaaattgttatccttcccagcgacagcgtgaggttaaacgatgtattaggggaccaaacccggctccctcgtaaaaggtggcgcgaggaccccctccccatgctgcggacgacgattgcgccgaaaacggcagcgcaaagagaacggctgctggacgctcttacgcaacttgcggatactgacccgcttttgcgttgcgaagtggattccatcacccatgagatcattctttcttttttgggccgggtgcagttggaggttgtttccgctttgctgtcggaaaaatacaagcttgaaacagtggtaaaggaaccctccgtcatttatatggagcggccgctcaaagcagccagccacaccatccatatcgaggtgccgcccaacccgttttgggcatccataggactgtctgttacaccactctcgcttggctccggtgtacaatacgagagccgggtttcgctgggatacttgaaccagagttttcaaaacgctgtcagggatggtatccgttacgggctggagcagggcttgttcggctggaacgtaacggactgtaagatttgctttgaatacgggctttattacagtccggtcagcacgccggcggacttccgctcattggccccgattgtattggaacaggcattgaaggaatcggggacgcagctgctggaaccttatctctccttcatcctctatgcgccccaggaatacctttccagggcttatcatgatgcaccgaaatactgtgccaccatcgaaacggcccaggtaaaaaaggatgaagttgtctttactggcgagattcccgcccgctgtatacaggcataccgtactgatctggccttttacaccaacgggcggagcgtatgccttacagagctgaaaggatatcaggccgctgtcggtcagccggtcatccagccccgccgtccaaacagccgcctggacaaggtgcgccatatgtttcagaaggtaatgtaa"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); expectedSeqid = "FR838949"; expectedSeq = "atgaaaataatcaatattggaattcttgcccatgtagacgctggaaagacgaccttgacggagagcctgctatatgccagcggagccatttcagaaccggggagcgtcgaaaaagggacaacgaggacggacaccatgtttttggagcggcagcgtgggattaccattcaagcggcagtcacttccttccagtggcacagatgtaaagttaacattgtggatacgcccggccacatggattttttggcggaggtgtaccgctctttggctgttttagatggggccatcttggtgatctccgctaaagatggcgtgcaggcccagacccgtattctgttccatgccctgcggaaaatgaacattcccaccgttatctttatcaacaagatcgaccaggctggcgttgatttgcagagcgtggttcagtctgttcgggataagctctccgccgatattatcatcaagcagacggtgtcgctgtccccggaaatagtcctggaggaaaataccgacatagaagcatgggatgcggtcatcgaaaataacgatgaattattggaaaagtatatcgcaggagaaccaatcagccgggaaaaacttgcgcgggaggaacagcggcgggttcaagacgcctccctgttcccggtctattatggcagcgccaaaaagggccttggcattcaaccgttgatggatgcggtgacagggctgttccaaccgattggggaacaggggagcgccgccctatgcggcagcgttttcaaggtggagtatacagattgcggccagcggcgtgtctatctacggctatacagcggaacgctgcgcctgcgggatacggtggccctggccgggagagaaaagctgaaaatcacagagatgcgtattccatccaaaggggaaattgttcggacagacaccgcttatccgggtgaaattgttatccttcccagcgacagcgtgaggttaaacgatgtattaggggacccaacccggctccctcgtaaaaggtggcgtgaggaccccctccccatgctgcggacgtcgattgcgccgaaaacggcagcgcaaagagaacggctgctggacgctcttacgcaacttgcggatactgacccgcttttgcgctgcgaggtggattccatcacccatgagatcattctttcttttttgggccgggtgcagttggaggttgtttccgctttgctgtcggaaaaatacaagcttgaaacagtggtaaaggaacccaccgtcatttatatggagcggccgctcaaagcagccagccacaccatccatatcgaggtgccgcccaacccgttttgggcatccatcggactgtctgttacaccactcccgcttggctccggtgtacaatacgagagccgggtttcgctgggatacttgaaccagagttttcaaaacgctgtcagggatggtatccgttacgggctggagcagggcttgttcggctggaacgtaacggactgtaagatttgctttgaatacgggctttattacagtccggtcagcacgccggcggacttccgctcattggccccgattgtattggaacaggcattgaaggaatcagggacgcaactgctggaaccttatctctccttcaccctctatgcgccccgggaatatctttccagggcttatcatgatgcaccgaaatactgtgccaccatcgaaacggtccaggtaaaaaaggatgaagttgtctttactggcgagattcccgcccgctgtatacaggcataccgtactgatctggccttttacaccaacgggcagagcgtatgccttacagaactgaaagggtatcaggccgctgtcggcaagccagtcatccagccccgccgtccaaacagccgcctggacaaggtgcgccatatgtttcagaaggtaatgtaa"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); assertNull(reader.readNextSequence()); } @Test public void testReadGenbank() throws IOException { SequenceReader reader = new SequenceReader(new File("test/test.genbank")); Sequence seq; String expectedSeqid; String expectedSeq; expectedSeqid = "S000349357"; expectedSeq = "gagtttgatcctggctcaggacgaacgctggcggcgtgcctaacacatgcaagccaaaggaaagtagcaatatgagtacttggcgcaagggtgcgtaatgtataggttatctacccttcggttcgggataacttcgcgaaagcgaagataataccggatattgaggagacttgaaagatttatcgccgaaggatgagcttatatcccatcaggtagttggtagggtaaaagcctaccaagcctacgacgggtagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtgaggaatattgctcaatgggtgaaagcctgaagcagcaacgccgcgtgaacgatgaaggtcttcggattgtaaagttcttttgcaggggacgaaaaactcgctttgcgagtctgacggtactctgcgaataagccacggctaactctgtgccagcagccgcggtgatacagaggtggcaagcgttgtccggatttactgggtgtaaagggtgcgtaggcggatttgcaagtcgggggttaaagactcttgcttaacaagagaaacgccttcgatactgcatgtctagagtgccgaagaggaaactggaatttccggtgtagcggtggaatgtgcagagatcggaaggaacaccagtggcgaaggcaggtttgtggtcggtaactgacgctgatgcacgaaagcgtggggagcaaacaggattagataccctggtagtccacgccctaaacgatggatgctagatgttggacttcggttcagtgtcgtagctaacgcagtaagcatcccacctggggagtacgcgcgcaagcgtgaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgatgcaacgcgaagaaccttacctaggcttgacatgctgggtaaagcggatgaaagtccgtgtccgaaagggatccagcacaggtgctgcatggctgtcgtcagctcgtgtcgtgagatgttgggttaagtcccgcaacgagcgcaacccctattgttagttgctaccaagtaatgttgagcactctagcaagactgcctacgcaagtagagaggaaggaggggatgacgtcaagtcctcatggcccttacgcctagggccacacacgtactacaatgggtactacaatgggcgaagtcgcgagacggaggtaatcccaaaaaagcactctcagttcagatcggagtctgcaactcgactccgtgaagttggaatcgctagtaatcgcggatcagcatgccgcggtgaatacgttcccgggccttgtacacaccgcccgtcaagccatggaagtcatcagcgcccgaagacgctttgcgtttaaggcgagggtggtaactggggctaagtcgtaacaaggtaac"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); expectedSeqid = "S002189637"; expectedSeq = "acacatgcagccaaaggaagtagcaatacgagtacttggcgtaagggtgagtaacgcataggtcatctgcccttaggttcgggataacttcgcgaaagcgaagataataccggatattgaggaaacttgaaagatttatcgcctaaggatgagcttatgtcccatcaggtagttggtagggtaaaagcctaccaagcctacgacgggtagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtgaggaatattgcgcaatgggtgaaagcctgacgcagcaacgccgcgtgtgcgacgaaggtcttcggattgtaaagcacttttgcaggggacgaacagcctattttatagacctgacggtaccttgcgaataagccacggctaactctgtgccagcagccgcggtgatacagaggtggcaagcgttgtccggatttactgggtataaagggtgcgtaggcggacctataagtcgagcgttaaagatcttcgcttaacgaagaaaatgcgctcgatactgttggtctagagtgttagagaggaaactggaatttccggtgtagcggtggaatgtgtagagatcggaaggaacaccagtggcgaaggcaggtttctggctaacaactgacgctgaggcacgaaagcgcgggtagcaaacaggattagataccctggtagtccgcgccctaaacgatggatgctagatgtcggacttcggttcggtgtcgcagctaacgcattaagcatcccacctgggaagtacgcgcgcaagcgtgaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgatgcaacgcgaagaaccttacctaggcttgacatggtagctaaggcggatgaaagtccgcgtccgaaagggagctatcacaggtgctgcatggctgtcgtcagctcgtgtcgtgagatgttgggttaagtcccgcaacgagcgcaacccctattgttagttgctaccgggtaatgccgagcactctagcaagactgcctacgcaagtagagaggaaggaggggatgacgtcaagtcctcatggcccttacgcctagggcaacacacgtactacaatgggcattacaatgggcgaaggcgcgagccggagataatcccaaaaaagtgctctcagttcagatcggagtctgcaactcgactccgtgaagttggaatcgctagtaatcgcaggtcagcatactgcggtgaatacgttcccgggccttgtacacaccgcccgtcaagccatggaagttatcggcgcccgaagacgcattgcgt"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); assertNull(reader.readNextSequence()); } @Test public void testReadCompressedFastaFile() throws IOException { SequenceReader reader = new SequenceReader(new File("test/test.fa.gz")); Sequence s = reader.readNextSequence(); assertEquals("test0", s.getSeqName()); assertEquals("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", s.getSeqString()); s = reader.readNextSequence(); assertEquals("test1", s.getSeqName()); assertEquals("aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~", s.getSeqString()); reader.close(); } @Test public void testReadCompressedFastqFile() throws IOException { String exp1Id = "001043_1783_0863"; String exp1Seq = "CTGATCATTGGGCGTAAAGAGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCGAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAAATACCCTCGTA"; String exp2Id = "001051_2436_2741"; String exp2Seq = "CATCTCACTGGGCATAAAGGGCACGCAGACGGACCGACAGGTCGTTTGTGAAAGGCGAGGGCTCAACCCTTGTTTGCGGACGAAACCGTCGGACTGGAGTACCGGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCCGGATACTGACGCTCAAGTGCGAAAGCTGGGGGAGCGAACGGGATTAGATACCCTTGTA"; SequenceReader seqFileReader = new SequenceReader(new File("test/test_init_v4.fastq.gz")); Sequence seq1 = seqFileReader.readNextSequence(); assertTrue(seq1 instanceof QSequence); assertEquals(exp1Id, seq1.getSeqName()); assertEquals(exp1Seq, seq1.getSeqString()); seq1 = seqFileReader.readNextSequence(); assertEquals(exp2Id, seq1.getSeqName()); assertEquals(exp2Seq, seq1.getSeqString()); } @Test public void testReadCompressedEMBL() throws IOException { SequenceReader reader = new SequenceReader(new File("test/test.embl.gz")); Sequence seq; String expectedSeqid; String expectedSeq; expectedSeqid = "FR838948"; expectedSeq = "atgaaaataatcaatattggaattcttgcccatgtagacgctggaaagacgaccttgacggagagcctgctatatgccagcggagccatttcagaaccggggagcgtcgaaaaagggacaacgaggacggacaccatgtttttggagcggcagcgtgggattaccattcaagcggcagtcacttccttccagtggcacagatgtaaagttaacattgtggatacgcccggccacatggattttttggcggaggtgtaccgctctttggctgttttagatggggccatcttggtgatctccgctaaagatggcgtgcaggcccagacccgtattctgttccatgccctgcggaaaatgaacattcccaccgttatctttatcaacaagatcgaccaggctggcgttgatttgcagagcgtggttcagtctgttcgggataagctctccgccgatattatcatcaagcagacggtgtcgctgtccccggaaatagtcctggaggaaaataccgacatagaagcatgggatgcggtcatcgaaaataacgatgaattattggaaaagtatatcgcaggagaaccaatcagccgggaaaaacttgcgcgggaggaacagcagcgggttcaagacgcctccctgttcccggtctatcatggcagcgccaaaaatggccttggcattcaaccgttgatggatgcggtgacagggctgttccaaccgattggggaacaggggggcgccgccctatgcggcagcgttttcaaggttgagtacaccgattgcggccagcggcgtgtctatctacggttatacagcggaacgctgcgcctgcgggatacggtggccctggccgggagagaaaagctgaaaatcacagagatgcgtattccatccaaaggggaaattgttcggacagacaccgcttatcagggtgaaattgttatccttcccagcgacagcgtgaggttaaacgatgtattaggggaccaaacccggctccctcgtaaaaggtggcgcgaggaccccctccccatgctgcggacgacgattgcgccgaaaacggcagcgcaaagagaacggctgctggacgctcttacgcaacttgcggatactgacccgcttttgcgttgcgaagtggattccatcacccatgagatcattctttcttttttgggccgggtgcagttggaggttgtttccgctttgctgtcggaaaaatacaagcttgaaacagtggtaaaggaaccctccgtcatttatatggagcggccgctcaaagcagccagccacaccatccatatcgaggtgccgcccaacccgttttgggcatccataggactgtctgttacaccactctcgcttggctccggtgtacaatacgagagccgggtttcgctgggatacttgaaccagagttttcaaaacgctgtcagggatggtatccgttacgggctggagcagggcttgttcggctggaacgtaacggactgtaagatttgctttgaatacgggctttattacagtccggtcagcacgccggcggacttccgctcattggccccgattgtattggaacaggcattgaaggaatcggggacgcagctgctggaaccttatctctccttcatcctctatgcgccccaggaatacctttccagggcttatcatgatgcaccgaaatactgtgccaccatcgaaacggcccaggtaaaaaaggatgaagttgtctttactggcgagattcccgcccgctgtatacaggcataccgtactgatctggccttttacaccaacgggcggagcgtatgccttacagagctgaaaggatatcaggccgctgtcggtcagccggtcatccagccccgccgtccaaacagccgcctggacaaggtgcgccatatgtttcagaaggtaatgtaa"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); expectedSeqid = "FR838949"; expectedSeq = "atgaaaataatcaatattggaattcttgcccatgtagacgctggaaagacgaccttgacggagagcctgctatatgccagcggagccatttcagaaccggggagcgtcgaaaaagggacaacgaggacggacaccatgtttttggagcggcagcgtgggattaccattcaagcggcagtcacttccttccagtggcacagatgtaaagttaacattgtggatacgcccggccacatggattttttggcggaggtgtaccgctctttggctgttttagatggggccatcttggtgatctccgctaaagatggcgtgcaggcccagacccgtattctgttccatgccctgcggaaaatgaacattcccaccgttatctttatcaacaagatcgaccaggctggcgttgatttgcagagcgtggttcagtctgttcgggataagctctccgccgatattatcatcaagcagacggtgtcgctgtccccggaaatagtcctggaggaaaataccgacatagaagcatgggatgcggtcatcgaaaataacgatgaattattggaaaagtatatcgcaggagaaccaatcagccgggaaaaacttgcgcgggaggaacagcggcgggttcaagacgcctccctgttcccggtctattatggcagcgccaaaaagggccttggcattcaaccgttgatggatgcggtgacagggctgttccaaccgattggggaacaggggagcgccgccctatgcggcagcgttttcaaggtggagtatacagattgcggccagcggcgtgtctatctacggctatacagcggaacgctgcgcctgcgggatacggtggccctggccgggagagaaaagctgaaaatcacagagatgcgtattccatccaaaggggaaattgttcggacagacaccgcttatccgggtgaaattgttatccttcccagcgacagcgtgaggttaaacgatgtattaggggacccaacccggctccctcgtaaaaggtggcgtgaggaccccctccccatgctgcggacgtcgattgcgccgaaaacggcagcgcaaagagaacggctgctggacgctcttacgcaacttgcggatactgacccgcttttgcgctgcgaggtggattccatcacccatgagatcattctttcttttttgggccgggtgcagttggaggttgtttccgctttgctgtcggaaaaatacaagcttgaaacagtggtaaaggaacccaccgtcatttatatggagcggccgctcaaagcagccagccacaccatccatatcgaggtgccgcccaacccgttttgggcatccatcggactgtctgttacaccactcccgcttggctccggtgtacaatacgagagccgggtttcgctgggatacttgaaccagagttttcaaaacgctgtcagggatggtatccgttacgggctggagcagggcttgttcggctggaacgtaacggactgtaagatttgctttgaatacgggctttattacagtccggtcagcacgccggcggacttccgctcattggccccgattgtattggaacaggcattgaaggaatcagggacgcaactgctggaaccttatctctccttcaccctctatgcgccccgggaatatctttccagggcttatcatgatgcaccgaaatactgtgccaccatcgaaacggtccaggtaaaaaaggatgaagttgtctttactggcgagattcccgcccgctgtatacaggcataccgtactgatctggccttttacaccaacgggcagagcgtatgccttacagaactgaaagggtatcaggccgctgtcggcaagccagtcatccagccccgccgtccaaacagccgcctggacaaggtgcgccatatgtttcagaaggtaatgtaa"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); assertNull(reader.readNextSequence()); } @Test public void testReadCompressedGenbank() throws IOException { SequenceReader reader = new SequenceReader(new File("test/test.genbank.gz")); Sequence seq; String expectedSeqid; String expectedSeq; expectedSeqid = "S000349357"; expectedSeq = "gagtttgatcctggctcaggacgaacgctggcggcgtgcctaacacatgcaagccaaaggaaagtagcaatatgagtacttggcgcaagggtgcgtaatgtataggttatctacccttcggttcgggataacttcgcgaaagcgaagataataccggatattgaggagacttgaaagatttatcgccgaaggatgagcttatatcccatcaggtagttggtagggtaaaagcctaccaagcctacgacgggtagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtgaggaatattgctcaatgggtgaaagcctgaagcagcaacgccgcgtgaacgatgaaggtcttcggattgtaaagttcttttgcaggggacgaaaaactcgctttgcgagtctgacggtactctgcgaataagccacggctaactctgtgccagcagccgcggtgatacagaggtggcaagcgttgtccggatttactgggtgtaaagggtgcgtaggcggatttgcaagtcgggggttaaagactcttgcttaacaagagaaacgccttcgatactgcatgtctagagtgccgaagaggaaactggaatttccggtgtagcggtggaatgtgcagagatcggaaggaacaccagtggcgaaggcaggtttgtggtcggtaactgacgctgatgcacgaaagcgtggggagcaaacaggattagataccctggtagtccacgccctaaacgatggatgctagatgttggacttcggttcagtgtcgtagctaacgcagtaagcatcccacctggggagtacgcgcgcaagcgtgaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgatgcaacgcgaagaaccttacctaggcttgacatgctgggtaaagcggatgaaagtccgtgtccgaaagggatccagcacaggtgctgcatggctgtcgtcagctcgtgtcgtgagatgttgggttaagtcccgcaacgagcgcaacccctattgttagttgctaccaagtaatgttgagcactctagcaagactgcctacgcaagtagagaggaaggaggggatgacgtcaagtcctcatggcccttacgcctagggccacacacgtactacaatgggtactacaatgggcgaagtcgcgagacggaggtaatcccaaaaaagcactctcagttcagatcggagtctgcaactcgactccgtgaagttggaatcgctagtaatcgcggatcagcatgccgcggtgaatacgttcccgggccttgtacacaccgcccgtcaagccatggaagtcatcagcgcccgaagacgctttgcgtttaaggcgagggtggtaactggggctaagtcgtaacaaggtaac"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); expectedSeqid = "S002189637"; expectedSeq = "acacatgcagccaaaggaagtagcaatacgagtacttggcgtaagggtgagtaacgcataggtcatctgcccttaggttcgggataacttcgcgaaagcgaagataataccggatattgaggaaacttgaaagatttatcgcctaaggatgagcttatgtcccatcaggtagttggtagggtaaaagcctaccaagcctacgacgggtagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtgaggaatattgcgcaatgggtgaaagcctgacgcagcaacgccgcgtgtgcgacgaaggtcttcggattgtaaagcacttttgcaggggacgaacagcctattttatagacctgacggtaccttgcgaataagccacggctaactctgtgccagcagccgcggtgatacagaggtggcaagcgttgtccggatttactgggtataaagggtgcgtaggcggacctataagtcgagcgttaaagatcttcgcttaacgaagaaaatgcgctcgatactgttggtctagagtgttagagaggaaactggaatttccggtgtagcggtggaatgtgtagagatcggaaggaacaccagtggcgaaggcaggtttctggctaacaactgacgctgaggcacgaaagcgcgggtagcaaacaggattagataccctggtagtccgcgccctaaacgatggatgctagatgtcggacttcggttcggtgtcgcagctaacgcattaagcatcccacctgggaagtacgcgcgcaagcgtgaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgatgcaacgcgaagaaccttacctaggcttgacatggtagctaaggcggatgaaagtccgcgtccgaaagggagctatcacaggtgctgcatggctgtcgtcagctcgtgtcgtgagatgttgggttaagtcccgcaacgagcgcaacccctattgttagttgctaccgggtaatgccgagcactctagcaagactgcctacgcaagtagagaggaaggaggggatgacgtcaagtcctcatggcccttacgcctagggcaacacacgtactacaatgggcattacaatgggcgaaggcgcgagccggagataatcccaaaaaagtgctctcagttcagatcggagtctgcaactcgactccgtgaagttggaatcgctagtaatcgcaggtcagcatactgcggtgaatacgttcccgggccttgtacacaccgcccgtcaagccatggaagttatcggcgcccgaagacgcattgcgt"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); assertNull(reader.readNextSequence()); } private static String readFully(BufferedReader reader) throws IOException { String line; StringBuilder ret = new StringBuilder(); while((line = reader.readLine()) != null) { ret.append(line).append("\n"); } return ret.toString(); } @Test public void testReadEMBLStream() throws IOException { String contents = readFully(new BufferedReader(new FileReader("test/test.embl"))); SequenceReader reader = new SequenceReader(new ByteArrayInputStream(contents.getBytes())); Sequence seq; String expectedSeqid; String expectedSeq; expectedSeqid = "FR838948"; expectedSeq = "atgaaaataatcaatattggaattcttgcccatgtagacgctggaaagacgaccttgacggagagcctgctatatgccagcggagccatttcagaaccggggagcgtcgaaaaagggacaacgaggacggacaccatgtttttggagcggcagcgtgggattaccattcaagcggcagtcacttccttccagtggcacagatgtaaagttaacattgtggatacgcccggccacatggattttttggcggaggtgtaccgctctttggctgttttagatggggccatcttggtgatctccgctaaagatggcgtgcaggcccagacccgtattctgttccatgccctgcggaaaatgaacattcccaccgttatctttatcaacaagatcgaccaggctggcgttgatttgcagagcgtggttcagtctgttcgggataagctctccgccgatattatcatcaagcagacggtgtcgctgtccccggaaatagtcctggaggaaaataccgacatagaagcatgggatgcggtcatcgaaaataacgatgaattattggaaaagtatatcgcaggagaaccaatcagccgggaaaaacttgcgcgggaggaacagcagcgggttcaagacgcctccctgttcccggtctatcatggcagcgccaaaaatggccttggcattcaaccgttgatggatgcggtgacagggctgttccaaccgattggggaacaggggggcgccgccctatgcggcagcgttttcaaggttgagtacaccgattgcggccagcggcgtgtctatctacggttatacagcggaacgctgcgcctgcgggatacggtggccctggccgggagagaaaagctgaaaatcacagagatgcgtattccatccaaaggggaaattgttcggacagacaccgcttatcagggtgaaattgttatccttcccagcgacagcgtgaggttaaacgatgtattaggggaccaaacccggctccctcgtaaaaggtggcgcgaggaccccctccccatgctgcggacgacgattgcgccgaaaacggcagcgcaaagagaacggctgctggacgctcttacgcaacttgcggatactgacccgcttttgcgttgcgaagtggattccatcacccatgagatcattctttcttttttgggccgggtgcagttggaggttgtttccgctttgctgtcggaaaaatacaagcttgaaacagtggtaaaggaaccctccgtcatttatatggagcggccgctcaaagcagccagccacaccatccatatcgaggtgccgcccaacccgttttgggcatccataggactgtctgttacaccactctcgcttggctccggtgtacaatacgagagccgggtttcgctgggatacttgaaccagagttttcaaaacgctgtcagggatggtatccgttacgggctggagcagggcttgttcggctggaacgtaacggactgtaagatttgctttgaatacgggctttattacagtccggtcagcacgccggcggacttccgctcattggccccgattgtattggaacaggcattgaaggaatcggggacgcagctgctggaaccttatctctccttcatcctctatgcgccccaggaatacctttccagggcttatcatgatgcaccgaaatactgtgccaccatcgaaacggcccaggtaaaaaaggatgaagttgtctttactggcgagattcccgcccgctgtatacaggcataccgtactgatctggccttttacaccaacgggcggagcgtatgccttacagagctgaaaggatatcaggccgctgtcggtcagccggtcatccagccccgccgtccaaacagccgcctggacaaggtgcgccatatgtttcagaaggtaatgtaa"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); expectedSeqid = "FR838949"; expectedSeq = "atgaaaataatcaatattggaattcttgcccatgtagacgctggaaagacgaccttgacggagagcctgctatatgccagcggagccatttcagaaccggggagcgtcgaaaaagggacaacgaggacggacaccatgtttttggagcggcagcgtgggattaccattcaagcggcagtcacttccttccagtggcacagatgtaaagttaacattgtggatacgcccggccacatggattttttggcggaggtgtaccgctctttggctgttttagatggggccatcttggtgatctccgctaaagatggcgtgcaggcccagacccgtattctgttccatgccctgcggaaaatgaacattcccaccgttatctttatcaacaagatcgaccaggctggcgttgatttgcagagcgtggttcagtctgttcgggataagctctccgccgatattatcatcaagcagacggtgtcgctgtccccggaaatagtcctggaggaaaataccgacatagaagcatgggatgcggtcatcgaaaataacgatgaattattggaaaagtatatcgcaggagaaccaatcagccgggaaaaacttgcgcgggaggaacagcggcgggttcaagacgcctccctgttcccggtctattatggcagcgccaaaaagggccttggcattcaaccgttgatggatgcggtgacagggctgttccaaccgattggggaacaggggagcgccgccctatgcggcagcgttttcaaggtggagtatacagattgcggccagcggcgtgtctatctacggctatacagcggaacgctgcgcctgcgggatacggtggccctggccgggagagaaaagctgaaaatcacagagatgcgtattccatccaaaggggaaattgttcggacagacaccgcttatccgggtgaaattgttatccttcccagcgacagcgtgaggttaaacgatgtattaggggacccaacccggctccctcgtaaaaggtggcgtgaggaccccctccccatgctgcggacgtcgattgcgccgaaaacggcagcgcaaagagaacggctgctggacgctcttacgcaacttgcggatactgacccgcttttgcgctgcgaggtggattccatcacccatgagatcattctttcttttttgggccgggtgcagttggaggttgtttccgctttgctgtcggaaaaatacaagcttgaaacagtggtaaaggaacccaccgtcatttatatggagcggccgctcaaagcagccagccacaccatccatatcgaggtgccgcccaacccgttttgggcatccatcggactgtctgttacaccactcccgcttggctccggtgtacaatacgagagccgggtttcgctgggatacttgaaccagagttttcaaaacgctgtcagggatggtatccgttacgggctggagcagggcttgttcggctggaacgtaacggactgtaagatttgctttgaatacgggctttattacagtccggtcagcacgccggcggacttccgctcattggccccgattgtattggaacaggcattgaaggaatcagggacgcaactgctggaaccttatctctccttcaccctctatgcgccccgggaatatctttccagggcttatcatgatgcaccgaaatactgtgccaccatcgaaacggtccaggtaaaaaaggatgaagttgtctttactggcgagattcccgcccgctgtatacaggcataccgtactgatctggccttttacaccaacgggcagagcgtatgccttacagaactgaaagggtatcaggccgctgtcggcaagccagtcatccagccccgccgtccaaacagccgcctggacaaggtgcgccatatgtttcagaaggtaatgtaa"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); assertNull(reader.readNextSequence()); } @Test public void testReadGenbankStream() throws IOException { String contents = readFully(new BufferedReader(new FileReader("test/test.genbank"))); SequenceReader reader = new SequenceReader(new ByteArrayInputStream(contents.getBytes())); Sequence seq; String expectedSeqid; String expectedSeq; expectedSeqid = "S000349357"; expectedSeq = "gagtttgatcctggctcaggacgaacgctggcggcgtgcctaacacatgcaagccaaaggaaagtagcaatatgagtacttggcgcaagggtgcgtaatgtataggttatctacccttcggttcgggataacttcgcgaaagcgaagataataccggatattgaggagacttgaaagatttatcgccgaaggatgagcttatatcccatcaggtagttggtagggtaaaagcctaccaagcctacgacgggtagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtgaggaatattgctcaatgggtgaaagcctgaagcagcaacgccgcgtgaacgatgaaggtcttcggattgtaaagttcttttgcaggggacgaaaaactcgctttgcgagtctgacggtactctgcgaataagccacggctaactctgtgccagcagccgcggtgatacagaggtggcaagcgttgtccggatttactgggtgtaaagggtgcgtaggcggatttgcaagtcgggggttaaagactcttgcttaacaagagaaacgccttcgatactgcatgtctagagtgccgaagaggaaactggaatttccggtgtagcggtggaatgtgcagagatcggaaggaacaccagtggcgaaggcaggtttgtggtcggtaactgacgctgatgcacgaaagcgtggggagcaaacaggattagataccctggtagtccacgccctaaacgatggatgctagatgttggacttcggttcagtgtcgtagctaacgcagtaagcatcccacctggggagtacgcgcgcaagcgtgaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgatgcaacgcgaagaaccttacctaggcttgacatgctgggtaaagcggatgaaagtccgtgtccgaaagggatccagcacaggtgctgcatggctgtcgtcagctcgtgtcgtgagatgttgggttaagtcccgcaacgagcgcaacccctattgttagttgctaccaagtaatgttgagcactctagcaagactgcctacgcaagtagagaggaaggaggggatgacgtcaagtcctcatggcccttacgcctagggccacacacgtactacaatgggtactacaatgggcgaagtcgcgagacggaggtaatcccaaaaaagcactctcagttcagatcggagtctgcaactcgactccgtgaagttggaatcgctagtaatcgcggatcagcatgccgcggtgaatacgttcccgggccttgtacacaccgcccgtcaagccatggaagtcatcagcgcccgaagacgctttgcgtttaaggcgagggtggtaactggggctaagtcgtaacaaggtaac"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); expectedSeqid = "S002189637"; expectedSeq = "acacatgcagccaaaggaagtagcaatacgagtacttggcgtaagggtgagtaacgcataggtcatctgcccttaggttcgggataacttcgcgaaagcgaagataataccggatattgaggaaacttgaaagatttatcgcctaaggatgagcttatgtcccatcaggtagttggtagggtaaaagcctaccaagcctacgacgggtagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtgaggaatattgcgcaatgggtgaaagcctgacgcagcaacgccgcgtgtgcgacgaaggtcttcggattgtaaagcacttttgcaggggacgaacagcctattttatagacctgacggtaccttgcgaataagccacggctaactctgtgccagcagccgcggtgatacagaggtggcaagcgttgtccggatttactgggtataaagggtgcgtaggcggacctataagtcgagcgttaaagatcttcgcttaacgaagaaaatgcgctcgatactgttggtctagagtgttagagaggaaactggaatttccggtgtagcggtggaatgtgtagagatcggaaggaacaccagtggcgaaggcaggtttctggctaacaactgacgctgaggcacgaaagcgcgggtagcaaacaggattagataccctggtagtccgcgccctaaacgatggatgctagatgtcggacttcggttcggtgtcgcagctaacgcattaagcatcccacctgggaagtacgcgcgcaagcgtgaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgatgcaacgcgaagaaccttacctaggcttgacatggtagctaaggcggatgaaagtccgcgtccgaaagggagctatcacaggtgctgcatggctgtcgtcagctcgtgtcgtgagatgttgggttaagtcccgcaacgagcgcaacccctattgttagttgctaccgggtaatgccgagcactctagcaagactgcctacgcaagtagagaggaaggaggggatgacgtcaagtcctcatggcccttacgcctagggcaacacacgtactacaatgggcattacaatgggcgaaggcgcgagccggagataatcccaaaaaagtgctctcagttcagatcggagtctgcaactcgactccgtgaagttggaatcgctagtaatcgcaggtcagcatactgcggtgaatacgttcccgggccttgtacacaccgcccgtcaagccatggaagttatcggcgcccgaagacgcattgcgt"; seq = reader.readNextSequence(); assertNotNull(seq); assertEquals(expectedSeqid, seq.getSeqName()); assertEquals(expectedSeq, seq.getSeqString()); assertNull(reader.readNextSequence()); } } ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/readers/core/000077500000000000000000000000001247756524500227525ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/readers/core/FastqCoreTest.java000066400000000000000000000133141247756524500263460ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.readers.core; import edu.msu.cme.rdp.readseq.QSequence; import edu.msu.cme.rdp.readseq.readers.IndexedSeqReader; import java.io.File; import java.io.IOException; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class FastqCoreTest { private static final String expectedSeqName = "001043_1783_0863"; private static final String expectedSeq = "CTGATCATTGGGCGTAAAGAGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCGAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAAATACCCTCGTA"; private static final byte[] expectedQual = new byte[]{27, 27, 27, 27, 27, 27, 27, 29, 26, 29, 28, 15, 27, 27, 27, 28, 27, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 29, 25, 27, 29, 25, 29, 28, 14, 27, 30, 26, 30, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 29, 28, 15, 27, 27, 27, 20, 7, 28, 27, 12, 27, 27, 27, 29, 26, 30, 26, 27, 29, 28, 15, 29, 26, 30, 26, 27, 27, 27, 29, 28, 14, 27, 27, 29, 25, 26, 27, 27, 23, 27, 27, 30, 26, 27, 27, 27, 25, 27, 27, 27, 27, 30, 26, 27, 27, 27, 27, 27, 26, 25, 22, 16, 7, 26, 26, 26, 30, 26, 29, 24, 29, 25, 27, 29, 25, 26, 27, 27, 27, 26, 27, 29, 24, 27, 27, 29, 28, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 29, 26, 26, 30, 26, 29, 25, 27, 25, 30, 26, 30, 26, 27, 29, 25, 27, 27, 30, 26, 30, 26, 27, 30, 26, 26, 26, 22, 15, 6, 26, 29, 26, 24, 27, 29, 28, 16, 26, 25, 27, 26, 26, 26, 25, 27, 27, 27, 27, 27, 30, 26, 26, 27, 27, 27, 29, 28, 17, 27, 27, 26, 27, 27, 27, 20, 7, 27, 26, 24, 29, 28, 15, 26, 27, 30, 26, 27, 29, 26, 28, 27, 17, 25, 23, 29, 28, 16, 25, 24, 27, 27, 24}; public FastqCoreTest() { } @Test public void test() throws IOException { File seqFile = new File(FastqCoreTest.class.getResource("/test_init_v4.fastq").getFile()); FastqCore core = new FastqCore(seqFile); QSequence seq = (QSequence) core.readNextSeq(); assertEquals("Sequence name doesn't match =(", expectedSeqName, seq.getSeqName()); assertEquals("Expected sequence doesn't match actual seq", expectedSeq, seq.getSeqString()); assertEquals("Quality sequence length doesn't match", expectedQual.length, seq.getQuality().length); for (int index = 0; index < expectedQual.length; index++) { assertEquals("Qual[" + index + "]", expectedQual[index], seq.getQuality()[index]); } // check the second sequence seq = (QSequence) core.readNextSeq(); assertEquals(seq.getSeqName(), "001051_2436_2741"); assertEquals(seq.getQuality()[0], 31); // the first quality score is @ assertEquals(seq.getQuality()[1], 27); // the first quality score is < // check the third sequence seq = (QSequence) core.readNextSeq(); assertEquals(seq.getSeqName(), "001053_1979_3818"); assertEquals(seq.getSeqString(), "CTGATCACTGGGCGTAAAGGGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCAAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGAGTA"); assertEquals(seq.getQuality()[0], 26); // the first quality score is ; assertEquals(seq.getQuality()[1], 27); // the first quality score is < seq = (QSequence) core.readNextSeq(); assertEquals(seq.getSeqName(), "001058_1806_1734"); assertEquals(seq.getSeqString(), "CATCTCATTGGGCATAAAGAGTGCGCAGGCGGTTGTGTGTGTCAGGTGTGAAGTCTCGGGGCTTAACTCCGAAACTGCGCCTGAAACTACACAACTAGAGTATTGGAGAGGGTAGCAGAATTCATGGTGTAGCAGTGAAATGCGTAGATATCATGAGGAATACCAGAGGCGAAGGCGGCTACCTGGACAATTACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAAAGGGATTAGATACCCCGGTA"); assertEquals(seq.getQuality()[0], 27); // the first quality score is < assertEquals(seq.getQuality()[1], 27); // the first quality score is < IndexedSeqReader reader = new IndexedSeqReader(seqFile); seq = (QSequence)reader.readSeq("001053_1979_3818"); assertEquals(seq.getSeqString(), "CTGATCACTGGGCGTAAAGGGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCAAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGAGTA"); assertEquals(seq.getQuality()[0], 26); // the first quality score is ; assertEquals(seq.getQuality()[1], 27); // the first quality score is < seq = (QSequence)reader.readSeq("001117_1940_3761"); assertEquals(seq.getSeqString(), "AGAGAGATTGGGTGTAAAGAGCGCGTAGGCGGTCCTGTAAGCCCGGCGTGAAAACCTGGAGCTCAACTCCGGGCCTGCGCTGGGAACTGCGGGACTAGAGTCATGGAAGGGAAGTTGGAATTCCAGGTGTAGGGGTGAAATCTGTAGATATCTGGAAGAACACCGGTGGCGAAGGCGAACTTCTGGCCAATGACTGACGCTGAGGCGCGAAAGTGCGGGAGCAAACAGGATTAGATACCCGTGTA"); assertEquals(seq.getQuality()[0], 20); // the first quality score is 5 assertEquals(seq.getQuality()[1], 24); // the first quality score is 9 } } ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/000077500000000000000000000000001247756524500215355ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/BarcodeUtilsTest.java000066400000000000000000000050061247756524500256210ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.utils.BarcodeUtils.BarcodeInvalidException; import java.io.StringReader; import java.util.Map; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class BarcodeUtilsTest { private static final String goodBarcode = "AAAA\ttest1\nTTTT\ttest2\nCCCC\ttest3"; private static final String badBarcode1 = "AAAA\ttest1\nAAAA\ttest2\nCCCC\ttest3"; private static final String badBarcode2 = "AAAA\ttest1\nAAA\ttest2\nCCCC\ttest3"; /** * Test of readBarcodeFile method, of class BarcodeUtils. */ @Test public void testGoodBarcode() throws Exception { try { Map barcodeMap = BarcodeUtils.readBarcodeFile(new StringReader(goodBarcode)); assertEquals(barcodeMap.get("aaaa"), "test1"); assertEquals(barcodeMap.get("tttt"), "test2"); assertEquals(barcodeMap.get("cccc"), "test3"); } catch(BarcodeInvalidException e) { fail("Good barcode failed: " + e.getMessage()); } } @Test public void testDupBarcode() throws Exception { try { Map barcodeMap = BarcodeUtils.readBarcodeFile(new StringReader(badBarcode1)); fail("Bad barcode (duplicate) passed when it shouldn't have"); } catch(BarcodeInvalidException e) { System.out.println(e.getMessage()); } } @Test public void testDupPrefixBarcode() throws Exception { try { Map barcodeMap = BarcodeUtils.readBarcodeFile(new StringReader(badBarcode2)); fail("Bad barcode (overlapping) passed when it shouldn't have"); } catch(BarcodeInvalidException e) { System.out.println(e.getMessage()); } } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/ProtTranslTest.java000066400000000000000000000032001247756524500253430ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class ProtTranslTest { @Test public void testProtTransl() { String seq = "actatggctatgcgtcaatgcgccctctacggcaaaggtggtatcggtaagtccaccactactcagaacctggtggcagccctggctgagatgggcaagaaggtcatgatcgttggttgtgacccgaaagctgactccacccgcctgatcctgcactccaaggcccagggcaccgtcatggaaatggccgcgtccgccggctcggtcgaagacctggagctggaagacgtgctgcagatcggcttcggcggcgtcaagtgcgtcgaatccggtggcccggagccgggcgtcggctgcgccggccgtggcgtgatcaccgcgatcaacttcctggaagaagaaggcgcctacagcgacgacctggacttcgtgttctatgacgtgctgggcgacgtggtatgcggc"; String expected = "tmamrqcalygkggigkstttqnlvaalaemgkkvmivgcdpkadstrlilhskaqgtvmemaasagsvedleledvlqigfggvkcvesggpepgvgcagrgvitainfleeegaysddldfvfydvlgdvvcg"; String transl = ProteinUtils.getInstance().translateToProtein(seq, false, 11); assertEquals(expected, transl); } } ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/SequenceFormatTest.java000066400000000000000000000035451247756524500261700ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import java.io.IOException; import edu.msu.cme.rdp.readseq.SequenceFormat; import edu.msu.cme.rdp.readseq.SequenceType; import java.io.File; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class SequenceFormatTest { @Test public void testSequenceFormatCheck() throws IOException { assertEquals(SequenceFormat.FASTA, SeqUtils.guessFileFormat(new File("test/test.fa"))); assertEquals(SequenceFormat.FASTQ, SeqUtils.guessFileFormat(new File("test/test_init_v4.fastq"))); assertEquals(SequenceFormat.STK, SeqUtils.guessFileFormat(new File("test/test.sto"))); assertEquals(SequenceFormat.SFF, SeqUtils.guessFileFormat(new File("test/454Reads.sff"))); } @Test public void testSequenceType() throws IOException { assertEquals(SequenceType.Nucleotide, SeqUtils.guessSequenceType(new File("test/test.fa"))); assertEquals(SequenceType.Nucleotide, SeqUtils.guessSequenceType(new File("test/test_init_v4.fastq"))); assertEquals(SequenceType.Protein, SeqUtils.guessSequenceType(new File("test/test.sto"))); } } ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/SequenceTrimmerTest.java000066400000000000000000000203641247756524500263550ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils; import edu.msu.cme.rdp.readseq.utils.BarcodeUtils.BarcodeInvalidException; import edu.msu.cme.rdp.readseq.readers.Sequence; import edu.msu.cme.rdp.readseq.utils.SequenceTrimmer.TrimStats; import java.io.StringReader; import java.util.Map; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class SequenceTrimmerTest { /** * Test of readBarcodeFile method, of class BarcodeUtils. */ @Test public void testTrimStats() throws Exception { String trimSeq1 = "aa..---GCTG..GAAT--cc.."; String trimSeq2 = "aaaaGCGTTGAngTTCTTCggac"; String trimSeq3 = "....---ACT-..------...."; String trimSeq4 = "....-------..---TTC...."; int trimStart = 3; int trimStop = 6; TrimStats trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq1), trimStart, trimStop); assertEquals("seq1 seqStart", 3, trimStats.seqStart); assertEquals("seq1 seqStop", 10, trimStats.seqStop); assertEquals("seq1 seqTrimStart", 3, trimStats.seqTrimStart); assertEquals("seq1 seqTrimStop", 6, trimStats.seqTrimStop); assertEquals("seq1 seqLength", 12, trimStats.seqLength); assertEquals("seq1 trimmedLength", 3, trimStats.trimmedLength); assertEquals("seq1 modelLength", 13, trimStats.modelLength); assertEquals("seq1 numNs", 0, trimStats.numNs); assertEquals("seq1 nsInTrim", 0, trimStats.nsInTrim); assertEquals("seq1 trimmed seq", "GCT", new String(trimStats.trimmedBases)); trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq2), trimStart, trimStop); assertEquals("seq2 seqStart", 0, trimStats.seqStart); assertEquals("seq2 seqStop", 12, trimStats.seqStop); assertEquals("seq2 seqTrimStart", 8, trimStats.seqTrimStart); assertEquals("seq2 seqTrimStop", 11, trimStats.seqTrimStop); assertEquals("seq2 seqLength", 23, trimStats.seqLength); assertEquals("seq2 trimmedLength", 3, trimStats.trimmedLength); assertEquals("seq2 modelLength", 13, trimStats.modelLength); assertEquals("seq2 numNs", 1, trimStats.numNs); assertEquals("seq2 nsInTrim", 0, trimStats.nsInTrim); assertEquals("seq2 trimmed seq", "TTG", new String(trimStats.trimmedBases)); trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq3), trimStart, trimStop); assertEquals("seq3 trimmed seq", "ACT", new String(trimStats.trimmedBases)); assertEquals("seq3 seqStart", 3, trimStats.seqStart); assertEquals("seq3 seqStop", 5, trimStats.seqStop); assertEquals("seq3 seqTrimStart", 1, trimStats.seqTrimStart); assertEquals("seq3 seqTrimStop", 3, trimStats.seqTrimStop); assertEquals("seq3 seqLength", 3, trimStats.seqLength); assertEquals("seq3 trimmedLength", 3, trimStats.trimmedLength); assertEquals("seq3 modelLength", 13, trimStats.modelLength); assertEquals("seq3 numNs", 0, trimStats.numNs); assertEquals("seq3 nsInTrim", 0, trimStats.nsInTrim); trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq4), trimStart, trimStop); assertEquals("seq4 trimmed seq", "---", new String(trimStats.trimmedBases)); assertEquals("seq4 seqStart", 10, trimStats.seqStart); assertEquals("seq4 seqStop", 12, trimStats.seqStop); assertEquals("seq4 seqTrimStart", 0, trimStats.seqTrimStart); assertEquals("seq4 seqTrimStop", 0, trimStats.seqTrimStop); assertEquals("seq4 seqLength", 3, trimStats.seqLength); assertEquals("seq4 trimmedLength", 0, trimStats.trimmedLength); assertEquals("seq4 modelLength", 13, trimStats.modelLength); assertEquals("seq4 numNs", 0, trimStats.numNs); assertEquals("seq4 nsInTrim", 0, trimStats.nsInTrim); assertEquals("gGG", SequenceTrimmer.trimMetaSeq("....aAUgGGT..AccTTC....", trimStart, trimStop)); assertEquals("-<,", SequenceTrimmer.trimMetaSeq("....[<<-<,-..->->>]....", trimStart, trimStop)); } /** * Test of readBarcodeFile method, of class BarcodeUtils. */ @Test public void testTrimStatsWithInsert() throws Exception { String trimSeq1 = "aa..---GCTG..GAAT--cc.."; String trimSeq2 = "aaaaGCGTTGAngTTCTTNggac"; String trimSeq3 = "....---ACT-..------...."; String trimSeq4 = "....-------..---TTC...."; int trimStart = 3; int trimStop = 9; TrimStats trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq1), trimStart, trimStop); assertEquals("seq1 seqStart", 3, trimStats.seqStart); assertEquals("seq1 seqStop", 10, trimStats.seqStop); assertEquals("seq1 seqTrimStart", 3, trimStats.seqTrimStart); assertEquals("seq1 seqTrimStop", 9, trimStats.seqTrimStop); assertEquals("seq1 seqLength", 12, trimStats.seqLength); assertEquals("seq1 trimmedLength", 6, trimStats.trimmedLength); assertEquals("seq1 modelLength", 13, trimStats.modelLength); assertEquals("seq1 numNs", 0, trimStats.numNs); assertEquals("seq1 nsInTrim", 0, trimStats.nsInTrim); assertEquals("seq1 trimmed seq", "GCTG..GA", new String(trimStats.trimmedBases)); trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq2), trimStart, trimStop); assertEquals("seq2 seqStart", 0, trimStats.seqStart); assertEquals("seq2 seqStop", 12, trimStats.seqStop); assertEquals("seq2 seqTrimStart", 8, trimStats.seqTrimStart); assertEquals("seq2 seqTrimStop", 16, trimStats.seqTrimStop); assertEquals("seq2 seqLength", 23, trimStats.seqLength); assertEquals("seq2 trimmedLength", 8, trimStats.trimmedLength); assertEquals("seq2 modelLength", 13, trimStats.modelLength); assertEquals("seq2 numNs", 2, trimStats.numNs); assertEquals("seq2 nsInTrim", 1, trimStats.nsInTrim); assertEquals("seq2 trimmed seq", "TTGAngTT", new String(trimStats.trimmedBases)); trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq3), trimStart, trimStop); System.err.println(new String(trimStats.trimmedBases)); assertEquals("seq3 seqStart", 3, trimStats.seqStart); assertEquals("seq3 seqStop", 5, trimStats.seqStop); assertEquals("seq3 seqTrimStart", 1, trimStats.seqTrimStart); assertEquals("seq3 seqTrimStop", 3, trimStats.seqTrimStop); assertEquals("seq3 seqLength", 3, trimStats.seqLength); assertEquals("seq3 trimmedLength", 3, trimStats.trimmedLength); assertEquals("seq3 modelLength", 13, trimStats.modelLength); assertEquals("seq3 nsInTrim", 0, trimStats.nsInTrim); assertEquals("seq3 numNs", 0, trimStats.numNs); trimStats = SequenceTrimmer.getStats(new Sequence("", "", trimSeq4), trimStart, trimStop); assertEquals("seq4 trimmed seq", "----..--", new String(trimStats.trimmedBases)); assertEquals("seq4 seqStart", 10, trimStats.seqStart); assertEquals("seq4 seqStop", 12, trimStats.seqStop); assertEquals("seq4 seqTrimStart", 0, trimStats.seqTrimStart); assertEquals("seq4 seqTrimStop", 0, trimStats.seqTrimStop); assertEquals("seq4 seqLength", 3, trimStats.seqLength); assertEquals("seq4 trimmedLength", 0, trimStats.trimmedLength); assertEquals("seq4 modelLength", 13, trimStats.modelLength); assertEquals("seq4 nsInTrim", 0, trimStats.nsInTrim); assertEquals("seq4 numNs", 0, trimStats.numNs); } @Test public void testCoordTranslation() { String trimSeq1 = "aa..---GCTGa.GAAT--cc.."; Sequence seq = new Sequence("", "", trimSeq1); assertEquals(1, SequenceTrimmer.translateCoord(1, seq, SequenceTrimmer.CoordType.seq, SequenceTrimmer.CoordType.seq)); assertEquals(0, SequenceTrimmer.translateCoord(1, seq, SequenceTrimmer.CoordType.seq, SequenceTrimmer.CoordType.model)); assertEquals(3, SequenceTrimmer.translateCoord(3, seq, SequenceTrimmer.CoordType.seq, SequenceTrimmer.CoordType.model)); assertEquals(7, SequenceTrimmer.translateCoord(7, seq, SequenceTrimmer.CoordType.seq, SequenceTrimmer.CoordType.model)); assertEquals(7, SequenceTrimmer.translateCoord(8, seq, SequenceTrimmer.CoordType.seq, SequenceTrimmer.CoordType.model)); } } ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/gbregion/000077500000000000000000000000001247756524500233315ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/gbregion/ComplementRegionTest.java000066400000000000000000000037551247756524500303150ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class ComplementRegionTest { private static final String seq = "acgtctagtagccggt"; private static final String expected = "AGACG"; private ComplementRegion regionTest = new ComplementRegion(new SimpleRegion("cat", 2, 6, Extends.EXACT)); /** * Test of toString method, of class ComplementRegion. */ @Test public void testToString() { assertEquals("complement(cat:2..6)", regionTest.toString()); } /** * Test of getId method, of class ComplementRegion. */ @Test public void testGetId() { assertEquals("cat", regionTest.getId()); } /** * Test of getSeqStart method, of class ComplementRegion. */ @Test public void testGetSeqStart() { assertEquals(2, regionTest.getSeqStart()); } /** * Test of getSeqStop method, of class ComplementRegion. */ @Test public void testGetSeqStop() { assertEquals(6, regionTest.getSeqStop()); } /** * Test of getSeqRegion method, of class ComplementRegion. */ @Test public void testGetSeqRegion() { assertEquals(expected, regionTest.getSeqRegion(seq)); } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/gbregion/JoinRegionTest.java000066400000000000000000000041431247756524500271010ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import java.util.Arrays; import java.util.List; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class JoinRegionTest { private static final String seq = "acgtctagtagccggt"; private static final String expected = "acgggt"; private static final JoinRegion regionTest = new JoinRegion("cat", (List)Arrays.asList(new SimpleRegion("cat", 1, 3, Extends.EXACT), new SimpleRegion("cat", 14, 16, Extends.EXACT)), false); /** * Test of toString method, of class JoinRegion. */ @Test public void testToString() { assertEquals("join(cat:1..3,cat:14..16)", regionTest.toString()); } /** * Test of getId method, of class JoinRegion. */ @Test public void testGetId() { assertEquals("cat", regionTest.getId()); } /** * Test of getSeqStart method, of class ComplementRegion. */ @Test public void testGetSeqStart() { assertEquals(1, regionTest.getSeqStart()); } /** * Test of getSeqStop method, of class ComplementRegion. */ @Test public void testGetSeqStop() { assertEquals(16, regionTest.getSeqStop()); } /** * Test of getSeqRegion method, of class ComplementRegion. */ @Test public void testGetSeqRegion() { assertEquals(expected, regionTest.getSeqRegion(seq)); } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/gbregion/RegionParserTest.java000066400000000000000000000046711247756524500274440ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class RegionParserTest { public RegionParserTest() { } @BeforeClass public static void setUpClass() throws Exception { } @AfterClass public static void tearDownClass() throws Exception { } /** * Test of parse method, of class RegionParser. */ @Test public void testParse() throws Exception { String str = "AB66732"; assertTrue(str.matches(RegionParser.accnoGiPattern)); str = "3532123"; assertTrue(str.matches(RegionParser.accnoGiPattern)); str = "asdfEAdf"; assertFalse(str.matches(RegionParser.accnoGiPattern)); str = "NC_009349.1:97292..97852"; assertEquals(str, RegionParser.parse(str).toString()); str = "97292..97852"; assertEquals(str, RegionParser.parse(str).toString()); str = "complement(NC_010473.1:4187575..>4188645)"; assertEquals(str, RegionParser.parse(str).toString()); str = "join(M33876.1:3924..4086,M33876.1:4146..4844,M33876.1:4905..4924)"; assertEquals(str, RegionParser.parse(str).toString()); str = "complement(join(BX294016.1:32656..33913,BX294016.1:33974..34061,BX294016.1:34124..34394))"; assertEquals(str, RegionParser.parse(str).toString()); str = "DQ783514.1:<1..>473"; assertEquals(str, RegionParser.parse(str).toString()); str = "DQ783514.1:<1..473"; assertEquals(str, RegionParser.parse(str).toString()); str = "DQ783514.1:1..>473"; assertEquals(str, RegionParser.parse(str).toString()); } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/gbregion/SimpleRegionTest.java000066400000000000000000000040061247756524500274310ustar00rootroot00000000000000/* * Copyright (C) 2012 Jordan Fish * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.gbregion; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; import static org.junit.Assert.*; /** * * @author fishjord */ public class SimpleRegionTest { private static final String seq = "acgtctagtagccggt"; private static final String expected = "agc"; private static final SimpleRegion regionTest = new SimpleRegion("cat", 10, 12, Extends.BEYOND_END); /** * Test of toString method, of class JoinRegion. */ @Test public void testToString() { assertEquals("cat:10..>12", regionTest.toString()); } /** * Test of getId method, of class JoinRegion. */ @Test public void testGetId() { assertEquals("cat", regionTest.getId()); } /** * Test of getSeqStart method, of class ComplementRegion. */ @Test public void testGetSeqStart() { assertEquals(10, regionTest.getSeqStart()); } /** * Test of getSeqStop method, of class ComplementRegion. */ @Test public void testGetSeqStop() { assertEquals(12, regionTest.getSeqStop()); } /** * Test of getSeqRegion method, of class ComplementRegion. */ @Test public void testGetSeqRegion() { assertEquals(expected, regionTest.getSeqRegion(seq)); } }ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/kmermatch/000077500000000000000000000000001247756524500235105ustar00rootroot00000000000000ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/kmermatch/NuclSeqMatchTest.java000066400000000000000000000026271247756524500275510ustar00rootroot00000000000000/* * Copyright (C) 2014 rdpstaff * */ package edu.msu.cme.rdp.readseq.utils.kmermatch; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.io.IOException; import java.util.ArrayList; import org.junit.Test; import static org.junit.Assert.*; /** * * @author wangqion */ public class NuclSeqMatchTest { public NuclSeqMatchTest() { } /** * Test of findTopKMatch method, of class NuclSeqMatch. */ @Test public void testFindTopKMatch() throws IOException { System.out.println("findTopKMatch"); ArrayList refList = new ArrayList(); refList.add(new Sequence("ref1", "", "cacgcgcctcatcctgcacgcaaaggccca")); refList.add(new Sequence("ref2", "", "cacgcgcctcGGcctgcacgGGcaaaggccca")); refList.add(new Sequence("ref3", "", "cacgcgcctcTTcctgcacgcaaaggccca")); Sequence queryseq = new Sequence("test", "", "cacgcgcctcatcctgcacgcaaaggccca"); int k = 3; NuclSeqMatch instance = new NuclSeqMatch(refList); ArrayList result = instance.findTopKMatch(queryseq, k); assertEquals("ref1", result.get(0).getBestMatch().getSeqName()); assertEquals("ref3", result.get(1).getBestMatch().getSeqName()); assertEquals(0.65, result.get(1).getSab(), 0.01); assertEquals("ref2", result.get(2).getBestMatch().getSeqName()); } } ReadSeq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/kmermatch/ProteinSeqMatchTest.java000066400000000000000000000052721247756524500302670ustar00rootroot00000000000000/* * Copyright (C) 2014 wangqion * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ package edu.msu.cme.rdp.readseq.utils.kmermatch; import edu.msu.cme.rdp.readseq.readers.Sequence; import java.util.ArrayList; import org.junit.Test; import static org.junit.Assert.*; /** * * @author wangqion */ public class ProteinSeqMatchTest { public ProteinSeqMatchTest() { } /** * Test of findTopKMatch method, of class ProteinSeqMatch. */ @Test public void testFindTopKMatch() { System.out.println("findTopKMatch"); ArrayList refList = new ArrayList(); refList.add(new Sequence("ref1", "", "aemgqkilivgcdpkadstrlilhakaqdtilslaasagsvedleledvmkvgyqdircvesggpepgvgcagrgvitsinfleengayenidyvs")); refList.add(new Sequence("ref3", "", "aemgqkilivgcdpkadstrlilhakxxaqdtilslxxaasagsvedlxxeledvmkvgyqdixxrcvesggpepgvgxxcagrgvitsinfleengayenidyvs")); refList.add(new Sequence("ref2", "", "aemgqkilivgcdpkadstrlilhakxxaqdtilslxxaasagsvedlxxeledvmkvgyqdircvesggpepgvgcagrgvitsinfleengayenidyvs")); Sequence queryseq = new Sequence("test", "", "cactcgtctgatcctgcacgccaaggcggcaggacaccatcctgagcctggcggccagcgccggcagcgtcgaggacctcgagctcgaggacgtgatgaaggtcggctaccagaacatccgttgcgtggaatccggcggtccggagcccggcgtcggctgtgccggccgcggcgtcatcacctcgatcaacttcctcgaagagaacggcgcctatgagga"); int k = 3; ProteinSeqMatch instance = new ProteinSeqMatch(refList, 4); ArrayList result = instance.findTopKMatch(queryseq, k); assertEquals("ref1", result.get(0).getBestMatch().getSeqName()); assertEquals("ref2", result.get(1).getBestMatch().getSeqName()); assertEquals("ref3", result.get(2).getBestMatch().getSeqName()); Sequence protSeq = new Sequence("test", "", "edlxxeledvmkvgyqdixxrcvesggp"); result = instance.findTopKMatch(protSeq, k); assertEquals("ref3", result.get(0).getBestMatch().getSeqName()); assertEquals("ref2", result.get(1).getBestMatch().getSeqName()); assertEquals("ref1", result.get(2).getBestMatch().getSeqName()); } } ReadSeq-2.0.2/test/test.embl000066400000000000000000000233011247756524500156560ustar00rootroot00000000000000ID FR838948; SV 1; linear; genomic DNA; STD; PRO; 1920 BP. XX AC FR838948; XX DT 08-JUN-2011 (Rel. 109, Created) DT 04-OCT-2011 (Rel. 110, Last updated, Version 2) XX DE Clostridium difficile tetW gene for tetracycline resistance protein, strain DE EII11 XX KW . XX OS Clostridium difficile OC Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; OC Clostridium. XX RN [1] RP 1-1920 RA Spigaglia P.; RT ; RL Submitted (08-MAR-2011) to the INSDC. RL Istituto Superiore di Sanita, Infectious Diseases, Viale Regina Elena 299, RL 00161 Rome, ITALY. XX RN [2] RA Spigaglia P., Barbanti F., Mastrantonio P.; RT "Multidrug resistance in European Clostridium difficile clinical isolates"; RL J. Antimicrob. Chemother. 66(10):2227-2234(2011). XX FH Key Location/Qualifiers FH FT source 1..1920 FT /organism="Clostridium difficile" FT /host="human" FT /strain="EII11" FT /mol_type="genomic DNA" FT /country="Hungary" FT /db_xref="taxon:1496" FT CDS 1..1920 FT /transl_table=11 FT /gene="tetW" FT /product="tetracycline resistance protein" FT /db_xref="UniProtKB/TrEMBL:F8KA51" FT /protein_id="CCA30602.1" FT /translation="MKIINIGILAHVDAGKTTLTESLLYASGAISEPGSVEKGTTRTDT FT MFLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDG FT VQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPE FT IVLEENTDIEAWDAVIENNDELLEKYIAGEPISREKLAREEQQRVQDASLFPVYHGSAK FT NGLGIQPLMDAVTGLFQPIGEQGGAALCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTV FT ALAGREKLKITEMRIPSKGEIVRTDTAYQGEIVILPSDSVRLNDVLGDQTRLPRKRWRE FT DPLPMLRTTIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVV FT SALLSEKYKLETVVKEPSVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLSLGSGV FT QYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFR FT SLAPIVLEQALKESGTQLLEPYLSFILYAPQEYLSRAYHDAPKYCATIETAQVKKDEVV FT FTGEIPARCIQAYRTDLAFYTNGRSVCLTELKGYQAAVGQPVIQPRRPNSRLDKVRHMF FT QKVM" XX SQ Sequence 1920 BP; 464 A; 486 C; 535 G; 435 T; 0 other; atgaaaataa tcaatattgg aattcttgcc catgtagacg ctggaaagac gaccttgacg 60 gagagcctgc tatatgccag cggagccatt tcagaaccgg ggagcgtcga aaaagggaca 120 acgaggacgg acaccatgtt tttggagcgg cagcgtggga ttaccattca agcggcagtc 180 acttccttcc agtggcacag atgtaaagtt aacattgtgg atacgcccgg ccacatggat 240 tttttggcgg aggtgtaccg ctctttggct gttttagatg gggccatctt ggtgatctcc 300 gctaaagatg gcgtgcaggc ccagacccgt attctgttcc atgccctgcg gaaaatgaac 360 attcccaccg ttatctttat caacaagatc gaccaggctg gcgttgattt gcagagcgtg 420 gttcagtctg ttcgggataa gctctccgcc gatattatca tcaagcagac ggtgtcgctg 480 tccccggaaa tagtcctgga ggaaaatacc gacatagaag catgggatgc ggtcatcgaa 540 aataacgatg aattattgga aaagtatatc gcaggagaac caatcagccg ggaaaaactt 600 gcgcgggagg aacagcagcg ggttcaagac gcctccctgt tcccggtcta tcatggcagc 660 gccaaaaatg gccttggcat tcaaccgttg atggatgcgg tgacagggct gttccaaccg 720 attggggaac aggggggcgc cgccctatgc ggcagcgttt tcaaggttga gtacaccgat 780 tgcggccagc ggcgtgtcta tctacggtta tacagcggaa cgctgcgcct gcgggatacg 840 gtggccctgg ccgggagaga aaagctgaaa atcacagaga tgcgtattcc atccaaaggg 900 gaaattgttc ggacagacac cgcttatcag ggtgaaattg ttatccttcc cagcgacagc 960 gtgaggttaa acgatgtatt aggggaccaa acccggctcc ctcgtaaaag gtggcgcgag 1020 gaccccctcc ccatgctgcg gacgacgatt gcgccgaaaa cggcagcgca aagagaacgg 1080 ctgctggacg ctcttacgca acttgcggat actgacccgc ttttgcgttg cgaagtggat 1140 tccatcaccc atgagatcat tctttctttt ttgggccggg tgcagttgga ggttgtttcc 1200 gctttgctgt cggaaaaata caagcttgaa acagtggtaa aggaaccctc cgtcatttat 1260 atggagcggc cgctcaaagc agccagccac accatccata tcgaggtgcc gcccaacccg 1320 ttttgggcat ccataggact gtctgttaca ccactctcgc ttggctccgg tgtacaatac 1380 gagagccggg tttcgctggg atacttgaac cagagttttc aaaacgctgt cagggatggt 1440 atccgttacg ggctggagca gggcttgttc ggctggaacg taacggactg taagatttgc 1500 tttgaatacg ggctttatta cagtccggtc agcacgccgg cggacttccg ctcattggcc 1560 ccgattgtat tggaacaggc attgaaggaa tcggggacgc agctgctgga accttatctc 1620 tccttcatcc tctatgcgcc ccaggaatac ctttccaggg cttatcatga tgcaccgaaa 1680 tactgtgcca ccatcgaaac ggcccaggta aaaaaggatg aagttgtctt tactggcgag 1740 attcccgccc gctgtataca ggcataccgt actgatctgg ccttttacac caacgggcgg 1800 agcgtatgcc ttacagagct gaaaggatat caggccgctg tcggtcagcc ggtcatccag 1860 ccccgccgtc caaacagccg cctggacaag gtgcgccata tgtttcagaa ggtaatgtaa 1920 // ID FR838949; SV 1; linear; genomic DNA; STD; PRO; 1920 BP. XX AC FR838949; XX DT 08-JUN-2011 (Rel. 109, Created) DT 04-OCT-2011 (Rel. 110, Last updated, Version 2) XX DE Clostridium difficile tetW gene for tetracycline resistance protein, strain DE CI7 XX KW . XX OS Clostridium difficile OC Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; OC Clostridium. XX RN [1] RP 1-1920 RA Spigaglia P.; RT ; RL Submitted (08-MAR-2011) to the INSDC. RL Istituto Superiore di Sanita, Infectious Diseases, Viale Regina Elena 299, RL 00161 Rome, ITALY. XX RN [2] RA Spigaglia P., Barbanti F., Mastrantonio P.; RT "Multidrug resistance in European Clostridium difficile clinical isolates"; RL J. Antimicrob. Chemother. 66(10):2227-2234(2011). XX FH Key Location/Qualifiers FH FT source 1..1920 FT /organism="Clostridium difficile" FT /host="human" FT /strain="CI7" FT /mol_type="genomic DNA" FT /country="Germany" FT /db_xref="taxon:1496" FT CDS 1..1920 FT /transl_table=11 FT /gene="tetW" FT /product="tetracycline resistance protein" FT /db_xref="UniProtKB/TrEMBL:F8KA52" FT /protein_id="CCA30603.1" FT /translation="MKIINIGILAHVDAGKTTLTESLLYASGAISEPGSVEKGTTRTDT FT MFLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDG FT VQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPE FT IVLEENTDIEAWDAVIENNDELLEKYIAGEPISREKLAREEQRRVQDASLFPVYYGSAK FT KGLGIQPLMDAVTGLFQPIGEQGSAALCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTV FT ALAGREKLKITEMRIPSKGEIVRTDTAYPGEIVILPSDSVRLNDVLGDPTRLPRKRWRE FT DPLPMLRTSIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVV FT SALLSEKYKLETVVKEPTVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLPLGSGV FT QYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFR FT SLAPIVLEQALKESGTQLLEPYLSFTLYAPREYLSRAYHDAPKYCATIETVQVKKDEVV FT FTGEIPARCIQAYRTDLAFYTNGQSVCLTELKGYQAAVGKPVIQPRRPNSRLDKVRHMF FT QKVM" XX SQ Sequence 1920 BP; 465 A; 487 C; 535 G; 433 T; 0 other; atgaaaataa tcaatattgg aattcttgcc catgtagacg ctggaaagac gaccttgacg 60 gagagcctgc tatatgccag cggagccatt tcagaaccgg ggagcgtcga aaaagggaca 120 acgaggacgg acaccatgtt tttggagcgg cagcgtggga ttaccattca agcggcagtc 180 acttccttcc agtggcacag atgtaaagtt aacattgtgg atacgcccgg ccacatggat 240 tttttggcgg aggtgtaccg ctctttggct gttttagatg gggccatctt ggtgatctcc 300 gctaaagatg gcgtgcaggc ccagacccgt attctgttcc atgccctgcg gaaaatgaac 360 attcccaccg ttatctttat caacaagatc gaccaggctg gcgttgattt gcagagcgtg 420 gttcagtctg ttcgggataa gctctccgcc gatattatca tcaagcagac ggtgtcgctg 480 tccccggaaa tagtcctgga ggaaaatacc gacatagaag catgggatgc ggtcatcgaa 540 aataacgatg aattattgga aaagtatatc gcaggagaac caatcagccg ggaaaaactt 600 gcgcgggagg aacagcggcg ggttcaagac gcctccctgt tcccggtcta ttatggcagc 660 gccaaaaagg gccttggcat tcaaccgttg atggatgcgg tgacagggct gttccaaccg 720 attggggaac aggggagcgc cgccctatgc ggcagcgttt tcaaggtgga gtatacagat 780 tgcggccagc ggcgtgtcta tctacggcta tacagcggaa cgctgcgcct gcgggatacg 840 gtggccctgg ccgggagaga aaagctgaaa atcacagaga tgcgtattcc atccaaaggg 900 gaaattgttc ggacagacac cgcttatccg ggtgaaattg ttatccttcc cagcgacagc 960 gtgaggttaa acgatgtatt aggggaccca acccggctcc ctcgtaaaag gtggcgtgag 1020 gaccccctcc ccatgctgcg gacgtcgatt gcgccgaaaa cggcagcgca aagagaacgg 1080 ctgctggacg ctcttacgca acttgcggat actgacccgc ttttgcgctg cgaggtggat 1140 tccatcaccc atgagatcat tctttctttt ttgggccggg tgcagttgga ggttgtttcc 1200 gctttgctgt cggaaaaata caagcttgaa acagtggtaa aggaacccac cgtcatttat 1260 atggagcggc cgctcaaagc agccagccac accatccata tcgaggtgcc gcccaacccg 1320 ttttgggcat ccatcggact gtctgttaca ccactcccgc ttggctccgg tgtacaatac 1380 gagagccggg tttcgctggg atacttgaac cagagttttc aaaacgctgt cagggatggt 1440 atccgttacg ggctggagca gggcttgttc ggctggaacg taacggactg taagatttgc 1500 tttgaatacg ggctttatta cagtccggtc agcacgccgg cggacttccg ctcattggcc 1560 ccgattgtat tggaacaggc attgaaggaa tcagggacgc aactgctgga accttatctc 1620 tccttcaccc tctatgcgcc ccgggaatat ctttccaggg cttatcatga tgcaccgaaa 1680 tactgtgcca ccatcgaaac ggtccaggta aaaaaggatg aagttgtctt tactggcgag 1740 attcccgccc gctgtataca ggcataccgt actgatctgg ccttttacac caacgggcag 1800 agcgtatgcc ttacagaact gaaagggtat caggccgctg tcggcaagcc agtcatccag 1860 ccccgccgtc caaacagccg cctggacaag gtgcgccata tgtttcagaa ggtaatgtaa 1920 //ReadSeq-2.0.2/test/test.embl.gz000066400000000000000000000047461247756524500163110ustar00rootroot00000000000000BxNtest.emblX]o۸}ϯ ij;Nk2W+QZeE2 +2 ln{ei89sf0Ɔwֻ,+Xfռur &A%]:-69=#>]wz~uj UNYuuu]y1z7['Lc[ab~WW-VKTR/%3UjY8+okm%ι$??z*6/cEżZl:fWvn՜zPc+gZ.fq/ÖPz > @>e/ڭo:N$#XK.ӕUwP r!ͫ}zJգ^/j /﯏&s|`G>C&CF{顼>iCfh5t??7Ec:G_9Yy } ;?82,j>ΫL㷯:oqY9=h%Z]c!&"Gq<̤," (+8s~ U""φH b" O8JSI^Bd<r8RHB $Aʣ"iVVA,3!4/2%~a8"LP0 TK0MU<ä"qI$#&r HDDaE6p(UJ%YÇ bC.yA"J$Y@4K!,$(d>2QQRs8jB-$NIbM"h|Ҥ.(L2%P@q1>YoǪĩEn E >>k1:BGI;fs2paplX6xpnhypbjXkCwpa/0iakwц/']2-=Gά6`#4! ! 8iM]m:GP֢Ch1Ô x:³CC=X B,) 7R%ܵuQ#4 &z&͎FhкuQpo֡C#t6+d(e07[`|XmI6d%J⎖"pqx. q"!Ta Pr@`:)(0;3<օeO\l: dEur(IYŽjL4/;*[P#e6ď-+ AvW[b_nB=D[A6RC{!myz{44bQLnawWݶ ⡣3f-M-K<Ķozߌ/(HLOH8 B!34z_Zrod'fa37ZpbgP3,# }){|^;=>"'\sz8׌0tԙ]݌/GC@ӈ1>Mdž8ƑN<4i#6e!MD,u~T!tYZShl|. M CJ64\@~8б8lyh1~ЩgH5о7 ! Te!ȉ?:m3}Z˗G(gT?M\!i.|CX;쭋<h1tT&MDzb4?MM3m: ^@C/GbGb6۳$5l,yy ٳ}=]^S;ײ"%{Z ZSk9kjVWZGyk䵳gy=k55y(yM]^^^6yI^sffbyM9 gy/kz#ksyzy}7yC~7#QϖE^7&&ReadSeq-2.0.2/test/test.fa000066400000000000000000000003231247756524500153240ustar00rootroot00000000000000>test0 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa >test1 aAcCgGtTuUmMrRwWsSyYkKvVhHdDbBxXnN-.~ >test2 ccccccccccccccccccccccccccccccccccccc >struct .-<({[])}>-. >mask 00000................1000000000A00000ReadSeq-2.0.2/test/test.fa.gz000066400000000000000000000002131247756524500157410ustar00rootroot00000000000000%Jtest.fa+I-.1J$pفr%:&;WFf{ex$9UDAx{$Gq%KJKtm4c5ktr @@ #qЉReadSeq-2.0.2/test/test.genbank000066400000000000000000000145551247756524500163570ustar00rootroot00000000000000LOCUS S000349357 1437 bp rRNA linear BCT 11-May-2004 DEFINITION uncultured Chlorobi bacterium; SM2A03. ACCESSION AF445706 REGION: <1..>1437 SOURCE uncultured Chlorobi bacterium ORGANISM uncultured Chlorobi bacterium Root; Bacteria; "Chlorobi"; "Chlorobia"; Chlorobiales; Chlorobiaceae; Chloroherpeton. REFERENCE 1 (bases 1 to 1437) AUTHORS Bonheyo G.T., Fouke B.W., Frias-Lopez J., Sanzenbacher B.; TITLE Microbial 16S rRNA diversity within travertine depositional facies from 73 degrees to 25 degreec C at Angel Terrace, Mammoth Hot Springs, Yellowstone National Park, USA JOURNAL Unpublished. REFERENCE 2 (bases 1 to 1437) AUTHORS Bonheyo G.T., Fouke B.W., Frias-Lopez J., Sanzenbacher B.; TITLE ; JOURNAL Submitted (08-NOV-2001) to the EMBL/GenBank/DDBJ databases. Geology, University of Illinois, Urbana-Champaign, 245 Natural History Building / 1301 W. Green Street, Urbana, IL 61801, USA COMMENT Genbank: AF445706 FEATURES Location/Qualifiers source 1..1437 /db_xref="taxon:156405" /mol_type="genomic DNA" /organism="uncultured Chlorobi bacterium" /clone="SM2A03" /environmental_sample="" rRNA <1..>1437 /product="16S ribosomal RNA" ORIGIN 1 gagtttgatc ctggctcagg acgaacgctg gcggcgtgcc taacacatgc aagccaaagg 61 aaagtagcaa tatgagtact tggcgcaagg gtgcgtaatg tataggttat ctacccttcg 121 gttcgggata acttcgcgaa agcgaagata ataccggata ttgaggagac ttgaaagatt 181 tatcgccgaa ggatgagctt atatcccatc aggtagttgg tagggtaaaa gcctaccaag 241 cctacgacgg gtagctggtc tgagaggatg atcagccaca ctggaactga gacacggtcc 301 agactcctac gggaggcagc agtgaggaat attgctcaat gggtgaaagc ctgaagcagc 361 aacgccgcgt gaacgatgaa ggtcttcgga ttgtaaagtt cttttgcagg ggacgaaaaa 421 ctcgctttgc gagtctgacg gtactctgcg aataagccac ggctaactct gtgccagcag 481 ccgcggtgat acagaggtgg caagcgttgt ccggatttac tgggtgtaaa gggtgcgtag 541 gcggatttgc aagtcggggg ttaaagactc ttgcttaaca agagaaacgc cttcgatact 601 gcatgtctag agtgccgaag aggaaactgg aatttccggt gtagcggtgg aatgtgcaga 661 gatcggaagg aacaccagtg gcgaaggcag gtttgtggtc ggtaactgac gctgatgcac 721 gaaagcgtgg ggagcaaaca ggattagata ccctggtagt ccacgcccta aacgatggat 781 gctagatgtt ggacttcggt tcagtgtcgt agctaacgca gtaagcatcc cacctgggga 841 gtacgcgcgc aagcgtgaaa ctcaaaggaa ttgacggggg cccgcacaag cggtggagta 901 tgtggtttaa ttcgatgcaa cgcgaagaac cttacctagg cttgacatgc tgggtaaagc 961 ggatgaaagt ccgtgtccga aagggatcca gcacaggtgc tgcatggctg tcgtcagctc 1021 gtgtcgtgag atgttgggtt aagtcccgca acgagcgcaa cccctattgt tagttgctac 1081 caagtaatgt tgagcactct agcaagactg cctacgcaag tagagaggaa ggaggggatg 1141 acgtcaagtc ctcatggccc ttacgcctag ggccacacac gtactacaat gggtactaca 1201 atgggcgaag tcgcgagacg gaggtaatcc caaaaaagca ctctcagttc agatcggagt 1261 ctgcaactcg actccgtgaa gttggaatcg ctagtaatcg cggatcagca tgccgcggtg 1321 aatacgttcc cgggccttgt acacaccgcc cgtcaagcca tggaagtcat cagcgcccga 1381 agacgctttg cgtttaaggc gagggtggta actggggcta agtcgtaaca aggtaac // LOCUS S002189637 1349 bp rRNA linear BCT 19-Jul-2010 DEFINITION uncultured bacterium; Be_050. ACCESSION FR667432 REGION: <1..>1349 SOURCE uncultured bacterium ORGANISM uncultured bacterium Root; Bacteria; "Chlorobi"; "Chlorobia"; Chlorobiales; Chlorobiaceae; Chloroherpeton. REFERENCE 1 (bases 1 to 1349) AUTHORS Bartrons M.; TITLE ; JOURNAL Submitted (15-JUL-2010) to the EMBL/GenBank/DDBJ databases. Bartrons M., Centre for Advanced Studies of Blanes (CEAB), Spanish Council for Scientific Research (CSIC), C/ d'acces a la Cala St. Francesc, 14, 17300, SPAIN. REFERENCE 2 AUTHORS Bartrons M.; TITLE Bacterial diversity from high mountain lake epilithic biofilms JOURNAL Unpublished. COMMENT Genbank: FR667432 FEATURES Location/Qualifiers source 1..1349 /organism="uncultured bacterium" /environmental_sample="" /mol_type="genomic DNA" /country="Spain:Pyrenees, Bergus" /lat_lon="42.59 N 0.96 E" /isolation_source="high mountain lake epilithic biofilm" /collection_date="29-Jul-2009" /clone="Be_050" /db_xref="taxon:77133" rRNA <1..>1349 /gene="16S rRNA" /product="16S ribosomal RNA" ORIGIN 1 acacatgcag ccaaaggaag tagcaatacg agtacttggc gtaagggtga gtaacgcata 61 ggtcatctgc ccttaggttc gggataactt cgcgaaagcg aagataatac cggatattga 121 ggaaacttga aagatttatc gcctaaggat gagcttatgt cccatcaggt agttggtagg 181 gtaaaagcct accaagccta cgacgggtag ctggtctgag aggatgatca gccacactgg 241 aactgagaca cggtccagac tcctacggga ggcagcagtg aggaatattg cgcaatgggt 301 gaaagcctga cgcagcaacg ccgcgtgtgc gacgaaggtc ttcggattgt aaagcacttt 361 tgcaggggac gaacagccta ttttatagac ctgacggtac cttgcgaata agccacggct 421 aactctgtgc cagcagccgc ggtgatacag aggtggcaag cgttgtccgg atttactggg 481 tataaagggt gcgtaggcgg acctataagt cgagcgttaa agatcttcgc ttaacgaaga 541 aaatgcgctc gatactgttg gtctagagtg ttagagagga aactggaatt tccggtgtag 601 cggtggaatg tgtagagatc ggaaggaaca ccagtggcga aggcaggttt ctggctaaca 661 actgacgctg aggcacgaaa gcgcgggtag caaacaggat tagataccct ggtagtccgc 721 gccctaaacg atggatgcta gatgtcggac ttcggttcgg tgtcgcagct aacgcattaa 781 gcatcccacc tgggaagtac gcgcgcaagc gtgaaactca aaggaattga cgggggcccg 841 cacaagcggt ggagtatgtg gtttaattcg atgcaacgcg aagaacctta cctaggcttg 901 acatggtagc taaggcggat gaaagtccgc gtccgaaagg gagctatcac aggtgctgca 961 tggctgtcgt cagctcgtgt cgtgagatgt tgggttaagt cccgcaacga gcgcaacccc 1021 tattgttagt tgctaccggg taatgccgag cactctagca agactgccta cgcaagtaga 1081 gaggaaggag gggatgacgt caagtcctca tggcccttac gcctagggca acacacgtac 1141 tacaatgggc attacaatgg gcgaaggcgc gagccggaga taatcccaaa aaagtgctct 1201 cagttcagat cggagtctgc aactcgactc cgtgaagttg gaatcgctag taatcgcagg 1261 tcagcatact gcggtgaata cgttcccggg ccttgtacac accgcccgtc aagccatgga 1321 agttatcggc gcccgaagac gcattgcgt // ReadSeq-2.0.2/test/test.genbank.gz000066400000000000000000000050031247756524500167620ustar00rootroot00000000000000yNtest.genbankXaSHί%U`,UR`6}AU%Jg6NWWW==zx;Lvw?='\VH]I+i{[Gg㋛Ȳ<.ALi-2 `8M!^oݗ\3'?v2Gߵ%r=9/W?3)x,v3~{u.免#9K4Ekk2:MFcFț{HzKBVM no>\OӲϥnZ;rV.?rb|J}?B҅tȱ42oJҟZ/iYVHމRyHJ}xt>S_DXs9PP}߼ E!&*aG|^ƙ|(KSӧ*+bGyB!Je?N:磦~<9>% /.YZ[oڇb$oA2:;OSW|{ZV [2Eze?('Iȯ-9$2'66wRa;1WWMP|~ږ[gd4]_P.KϬtyiѢ\V>]k$|p{>lG{YK2OvHryy?l\Vb~viϵ2O_m_,i]~<:ݴ}SU>,}z8 ^^sz'Q8C#,+8faFo3 ;Q{ol% ߃\#qcw1 bc0Z:0AGE."'!/c==SsN/ӕ h]Ӷ;Cc.X¦Ǒ*N Ȍ%bhg 0uFRd8RDT맶S= Z/!+8QtuP@(0#A(">ԵWC=1, U l'^xV [zguJp.Zq.k17aQT1VŬRX\DTP+8X~DU˰/zbj{>?AdGFD=܅sd>h6)Զ-COh-()5| 獭C0 uD8Ly2xuRtã~Q]asq+Kڛ͚9MzlWzFݤg~(cՋn**Zd%z;2TVXV2x q14w^o?^AQ*YNSUAET^e.:L'O/:y'V{Nr'CwgX&smuO+s6Yפu, 3ѩ˝j)ˡgc7Sꏪo}M˿K4/)g%*wP Ŧiw*N{:hlQ: n9SOsMXi_Hk]fI]a9 }Zfi JCex {;DLƒ$״iEkTGE&oٓŚ8cм k"4g]eȏa =uqƠ=Vhp%Iݸ*3<胉=Ƨ"q@uC9c d`1ΎaO ~D"&0 Mfo1:S+cr&V0#q&bB4vD'+iX[structmaskReadSeq-2.0.2/test/test.sto000066400000000000000000000026561247756524500155560ustar00rootroot00000000000000# STOCKHOLM 1.0 GF040U105F9RVG TRLILNSKAQTTVMDLARERGTVEDLELEDVSVEGHLGVRCAESGGPEPG #=GR GF040U105F9RVG PP 9************************************************* GF040U105FRBRW TRLILNSKAQTTVMDLARERGTVEDLELKDVLVEGHLGVRCAESGGPEPG #=GR GF040U105FRBRW PP 9************************************************* GF040U105FT65L TRLILHAKAQTTVMDLVRELGTVEDLELEDVMKVGYGDVKCVESGGPEPG #=GR GF040U105FT65L PP 9************************************************* #=GC PP_cons 9************************************************* #=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx GF040U105F9RVG VGCAGRGVITAINFLEENGAYTEdTDYVFYDVLGDVVCGGFAMPIRENKA #=GR GF040U105F9RVG PP *********************988************************** GF040U105FRBRW VGCAGRGVITAINFLEENGAYTEdTDYVFYDVLGDVVCGGFAMPIRENKA #=GR GF040U105FRBRW PP *********************988************************** GF040U105FT65L VGCAGRGVITAINFLEENGAYTPdLDFVFYDVLGDVVCGGFSMPIRENKA #=GR GF040U105FT65L PP *********************977************************** #=GC PP_cons *********************98.************************** #=GC RF xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx GF040U105F9RVG KEIYIVT #=GR GF040U105F9RVG PP ******7 GF040U105FRBRW KEIYIVT #=GR GF040U105FRBRW PP ******7 GF040U105FT65L EEIYIVC #=GR GF040U105FT65L PP *****97 #=GC PP_cons ******7 #=GC RF xxxxxxx // ReadSeq-2.0.2/test/test_1.fa000066400000000000000000000002271247756524500155470ustar00rootroot00000000000000>test0 aaaaaaaaaaaaaaaaaa aaaaaaaaa aaaaaaaaaa >test1 aAcCgGtTuUmMrRw WsSyYkKvVhHdDbBxXnN-.~ >test2 ccccccccccccccccccccc ccccccccccccccccReadSeq-2.0.2/test/test_init_v4.fastq000066400000000000000000000122001247756524500175050ustar00rootroot00000000000000@001043_1783_0863 CTGATCATTGGGCGTAAAGAGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCGAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAAATACCCTCGTA +001043_1783_0863 <<<<<<<>;>=0<<<=<-<<<<<<<<<>:<>:>=/=0<<<5(=<-<<<>;?;<>=0>;?;<<<>=/<<>:;<<8<9>:<>:;<<<;<>9<<>=1<<<<<<<<<<<<<>;;?;>:<:?;?;<>:<;9<>=1;:<;;;:<<<<=2<<;<<<5(<;9>=0;;=<2:8>=1:9<<9 @001051_2436_2741 CATCTCACTGGGCATAAAGGGCACGCAGACGGACCGACAGGTCGTTTGTGAAAGGCGAGGGCTCAACCCTTGTTTGCGGACGAAACCGTCGGACTGGAGTACCGGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCCGGATACTGACGCTCAAGTGCGAAAGCTGGGGGAGCGAACGGGATTAGATACCCTTGTA + @<<<<<<<<<=-<<<>=/<;,<<;<<<<;<=8;?;<<<<;6<<<=<-;<<=<,>:8;<><.<<<>;>=0>:;>=/<<=8<<<>=0>;<;<>:6<<>:<;<;>;>;<<:=<->9<<>:<7>;>=0=9<<<<<;>:<<=<,<;<<<;<<<9<<>=1;<<>;<<;?;<<=9=9:>;:>:>;;<;<<<<<;<<<=0<<<;:7/%<<<=2;=8<<<<<>=2>;<<: @001053_1979_3818 CTGATCACTGGGCGTAAAGGGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCAAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGAGTA + ;<;<<<<<;><.;<:=<,;:*9<;<9:=9<=9>=/;>;>::8<<:<<<<;=<-<;;3$=<.:;7=8=9:;9(=9>:<<<<:*<;>9<:<89>=19<<<::<:<8<<<;<::70(5<9;6:5;6<=8:4<<;;:4<:>=0;<<:<<;<<<;<:?;<<8;<>:>;<>;;:7/%:?;<<<;+8<<;<<<;:53=08<<<=<6(<:<>=2;6?;<>:;;5<<>=1878;; @001058_1806_1734 CATCTCATTGGGCATAAAGAGTGCGCAGGCGGTTGTGTGTGTCAGGTGTGAAGTCTCGGGGCTTAACTCCGAAACTGCGCCTGAAACTACACAACTAGAGTATTGGAGAGGGTAGCAGAATTCATGGTGTAGCAGTGAAATGCGTAGATATCATGAGGAATACCAGAGGCGAAGGCGGCTACCTGGACAATTACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAAAGGGATTAGATACCCCGGTA +001058_1806_1734 <<<<<<<>:>=0<<<=<.<<<<<<<<<=9<>:>:<<<<<<<<<:=9<<>:<=<-<;<<<>:<<=<-<<<<<<=9<<<<;;<<>:>;;<<>=1;<<<<;>:?;<<=0<<<<:<:;<<:<<<<;>:>:<<>:<;<>:;;<;<>::?;;<=9?;<<:;<;<:<<<>:<9<<;:);:;;<<5(<<<=<6*>=23?;;<;<<=<6)>;;< @001061_1763_1394 CATCTCATGGGTGTAAAGAGCACGCAGGCGGACCGACAGGTCGTTTGTGAAAGGCGAGGGCTCAACCCTTGTTTGCGGACGAAACCGTCGGACTGGAGTACCGGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCCGGATACTGACACTCAAGTGCGAAAGCTGGGGGAGCGAACGGGATTAGATACCCGTGTA +001061_1763_1394 <<<<<<<0>=0<<<=<-<<;<<<;<9;>:<<<<=9<<<=<.<<<=<.>:<;<=<-<;=/>:<=<.<<=9<<<><.>:;<<=9<<<>;<<<<>:>;<<:<;+>9<<>9?;>:>=/?;<<<<;<>:<<=<-<;<<<:<<<<<<>=1<>:?;<<>;<<<>;<;>;?;<=;;>;=;<>;<:>;<<<<9<<<<<<;>;<<<;;>=1;<<;;7/&96<;?;<>=27>;;9;;9>=1<9<:: @001071_2308_3096 CTGATCACTGGGNTAAAGGGTGCGCAGGCGGTTGTGTGTGTCAGGTGTGAAATCTCGGGGCTTAACTCCGAAACTGCGCCTGAAACTACACAACTAGAGTATTGGAGAGGGTAGCAGAATTCATGGTGTAGCAGTGAAATGCGTAGATATCATGAGGAATACCAGAGGCGAAGGCGGCTACCTGGACAATTACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAAAGGGATTAGATACCCCTGTA +001071_2308_3096 <<<<<<<<<>=/!/<;+<;+<<<<<;?;<>;>9<;<<<;;<<;>:<;<<;:)<<<<<;4U'>;>:::>:<;9(<<<<<>:<<;:*<<<<<<>:<<<<9;<<>;?;<;<><.;;:<<<>9?;:<<>;<9<<<<;;;:=<-<<<<<;<;<<<<<<;;>;=9;<>;9<;>:<:<>;;;;>;;<8<<<<;4&087; @001097_1674_1560 CATGAGATTGGGCTTAAAGGGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCTGGGCTCAACCTAGGAATAGCATTTCGAACTGGCGAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCATGCACGAAAGCGTGGGGAGCAGACAGGATTAGATACCCTAGTA +001097_1674_1560 <9<<<7;?;>=17=9>=1=<.<<<<<<=9<>;=<.;>;=9<8;;<:<<<<=<-<;9(998%<<<=9?;;794>:;<9<:=<-<<>;;<81<;?;<<:8<<;;?;:<87<;;70'<<6<8:4=9;<>:?;9;>;?;<;6<:>:>;<>;;:6.$:=<-!<<=<.<<<<<<<<<>:<=9>=.;<<<<<<<<<<>=/<<<5(<;+<<<>;>;<=<->:?;<<<>=/<<>;<<<8<:<<<<<;:70(:;<>:=9>:<=9<<<<;;=9<<>=1<<<<<<<<<<<<:<9>;>;:>9<<>;?;<>;;:7/&<>;:;>=0<<<<:;<<<<<<=9;<<<>=0<;;<<<4&<<:>=1<;?;=0<:<;8 @001103_1821_2690 CATGAGATTGGGTGTAAAGCGTGCGCAGGCGGTTTGTTAAGCGAGATGTGAAAGCCCCGGGCTCAACCTGGGAATTGCATTTCGAACTGGCGAACTAGAGTCTTGTAGAGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGTGTA +001103_1821_2690 <:<<<<<>:>=.<<<=<-<<<<<<<<<>:<>:=<.;<<<<<<<<<<>=/<<<5(=<-<<<.>:>;<<<>=.<<>:<<<7<;?;<<<;<<;:>:>:<=8<<<<<;>:<<>=1<<<<<<<<<<<<<>:;>;?;<9?;>;<>:<<>:>:;7;>=1;<<<:<<<<<;<>:;<<;>=0<<<<<;4%<99>=/<;9:;;9=<.<(<<9 @001117_1940_3761 AGAGAGATTGGGTGTAAAGAGCGCGTAGGCGGTCCTGTAAGCCCGGCGTGAAAACCTGGAGCTCAACTCCGGGCCTGCGCTGGGAACTGCGGGACTAGAGTCATGGAAGGGAAGTTGGAATTCCAGGTGTAGGGGTGAAATCTGTAGATATCTGGAAGAACACCGGTGGCGAAGGCGAACTTCTGGCCAATGACTGACGCTGAGGCGCGAAAGTGCGGGAGCAAACAGGATTAGATACCCGTGTA +001117_1940_3761 59;<;<<>;>=18<;==2:<<;<<9<;;?;<<<>;:>=0>;;;<<<<6+;9<>;<<;<;?;2<>;>=1?;;<9<;<>=1?;:<9:>=1<:<9:<<;<<<>;>;>=1?;9>;?;?;?;>;=0<<<<<<<:<<;;<=9=9<>;<;>:>9<:5:;<8:57;:4;;6;871;6938;9<6899;;945705:5697#9828==258297"904,04,;811797-"1015 ReadSeq-2.0.2/test/test_init_v4.fastq.gz000066400000000000000000000032511247756524500201320ustar00rootroot00000000000000Ktest_init_v4.fastqXr8/MNdRIJa[Nܳ/[٭ڪ}ɲD4Әn[Uձ}h.U蚇ieei^qy4a^г!^48M~ r7 M@͜^-@~qRiAZݓOZWG:v򅁘UNv*|k^_ixg;[6k`'c8V 9%Ѧ[摆u}4*q8ú>"M,e4h viE,66C H+>|cr86뇉@N 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