Bio-Cluster-1.7.3000755000765000024 013354321744 13727 5ustar00cjfieldsstaff000000000000Changes100644000765000024 33213354321744 15261 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3Summary of important user-visible changes for Bio-Cluster --------------------------------------------------------- 1.7.3 2018-09-30 23:34:41-05:00 America/Chicago * First release after split from bioperl-live. LICENSE100644000765000024 4523313354321744 15044 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3This software is copyright (c) 2018 by Allen Day , Andrew Macgregor , David Green, GNF -- Genomics Institute of the Novartis Research Foundation, Hilmar Lapp , Jo-Ann Stanton, Shawn Hoon , Stan Nelson . This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. Terms of the Perl programming language system itself a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or b) the "Artistic License" --- The GNU General Public License, Version 1, February 1989 --- This software is Copyright (c) 2018 by Allen Day , Andrew Macgregor , David Green, GNF -- Genomics Institute of the Novartis Research Foundation, Hilmar Lapp , Jo-Ann Stanton, Shawn Hoon , Stan Nelson . This is free software, licensed under: The GNU General Public License, Version 1, February 1989 GNU GENERAL PUBLIC LICENSE Version 1, February 1989 Copyright (C) 1989 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The license agreements of most software companies try to keep users at the mercy of those companies. By contrast, our General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. The General Public License applies to the Free Software Foundation's software and to any other program whose authors commit to using it. You can use it for your programs, too. When we speak of free software, we are referring to freedom, not price. Specifically, the General Public License is designed to make sure that you have the freedom to give away or sell copies of free software, that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of a such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must tell them their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License Agreement applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any work containing the Program or a portion of it, either verbatim or with modifications. Each licensee is addressed as "you". 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this General Public License and to the absence of any warranty; and give any other recipients of the Program a copy of this General Public License along with the Program. You may charge a fee for the physical act of transferring a copy. 2. You may modify your copy or copies of the Program or any portion of it, and copy and distribute such modifications under the terms of Paragraph 1 above, provided that you also do the following: a) cause the modified files to carry prominent notices stating that you changed the files and the date of any change; and b) cause the whole of any work that you distribute or publish, that in whole or in part contains the Program or any part thereof, either with or without modifications, to be licensed at no charge to all third parties under the terms of this General Public License (except that you may choose to grant warranty protection to some or all third parties, at your option). c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the simplest and most usual way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this General Public License. d) You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 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(This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form alone.) Source code for a work means the preferred form of the work for making modifications to it. For an executable file, complete source code means all the source code for all modules it contains; but, as a special exception, it need not include source code for modules which are standard libraries that accompany the operating system on which the executable file runs, or for standard header files or definitions files that accompany that operating system. 4. You may not copy, modify, sublicense, distribute or transfer the Program except as expressly provided under this General Public License. Any attempt otherwise to copy, modify, sublicense, distribute or transfer the Program is void, and will automatically terminate your rights to use the Program under this License. However, parties who have received copies, or rights to use copies, from you under this General Public License will not have their licenses terminated so long as such parties remain in full compliance. 5. By copying, distributing or modifying the Program (or any work based on the Program) you indicate your acceptance of this license to do so, and all its terms and conditions. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. 7. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of the license which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the license, you may choose any version ever published by the Free Software Foundation. 8. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 9. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 10. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE 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. END OF TERMS AND CONDITIONS Appendix: How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to humanity, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) 19yy 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 1, 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, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) 19xx name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (a program to direct compilers to make passes at assemblers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice That's all there is to it! --- The Artistic License 1.0 --- This software is Copyright (c) 2018 by Allen Day , Andrew Macgregor , David Green, GNF -- Genomics Institute of the Novartis Research Foundation, Hilmar Lapp , Jo-Ann Stanton, Shawn Hoon , Stan Nelson . This is free software, licensed under: The Artistic License 1.0 The Artistic License Preamble The intent of this document is to state the conditions under which a Package may be copied, such that the Copyright Holder maintains some semblance of artistic control over the development of the package, while giving the users of the package the right to use and distribute the Package in a more-or-less customary fashion, plus the right to make reasonable modifications. Definitions: - "Package" refers to the collection of files distributed by the Copyright Holder, and derivatives of that collection of files created through textual modification. - "Standard Version" refers to such a Package if it has not been modified, or has been modified in accordance with the wishes of the Copyright Holder. - "Copyright Holder" is whoever is named in the copyright or copyrights for the package. - "You" is you, if you're thinking about copying or distributing this Package. - "Reasonable copying fee" is whatever you can justify on the basis of media cost, duplication charges, time of people involved, and so on. (You will not be required to justify it to the Copyright Holder, but only to the computing community at large as a market that must bear the fee.) - "Freely Available" means that no fee is charged for the item itself, though there may be fees involved in handling the item. It also means that recipients of the item may redistribute it under the same conditions they received it. 1. You may make and give away verbatim copies of the source form of the Standard Version of this Package without restriction, provided that you duplicate all of the original copyright notices and associated disclaimers. 2. You may apply bug fixes, portability fixes and other modifications derived from the Public Domain or from the Copyright Holder. A Package modified in such a way shall still be considered the Standard Version. 3. 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However, you may distribute this Package in aggregate with other (possibly commercial) programs as part of a larger (possibly commercial) software distribution provided that you do not advertise this Package as a product of your own. 6. The scripts and library files supplied as input to or produced as output from the programs of this Package do not automatically fall under the copyright of this Package, but belong to whomever generated them, and may be sold commercially, and may be aggregated with this Package. 7. C or perl subroutines supplied by you and linked into this Package shall not be considered part of this Package. 8. The name of the Copyright Holder may not be used to endorse or promote products derived from this software without specific prior written permission. 9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. The End dist.ini100644000765000024 137013354321744 15455 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3name = Bio-Cluster version = 1.7.3 author = Allen Day author = Andrew Macgregor author = David Green author = Hilmar Lapp author = Jo-Ann Stanton author = Shawn Hoon author = Stan Nelson copyright_holder = Allen Day , Andrew Macgregor , David Green, GNF -- Genomics Institute of the Novartis Research Foundation, Hilmar Lapp , Jo-Ann Stanton, Shawn Hoon , Stan Nelson license = Perl_5 ;; Modules should be fixed so that these don't have to be removed. [@BioPerl] -remove = PodCoverageTests -remove = PodWeaver -remove = Test::EOL -remove = Test::NoTabs META.yml100644000765000024 1657713354321744 15321 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3--- abstract: 'BioPerl cluster modules' author: - 'Allen Day ' - 'Andrew Macgregor ' - 'David Green' - 'Hilmar Lapp ' - 'Jo-Ann Stanton' - 'Shawn Hoon ' - 'Stan Nelson ' build_requires: Bio::Root::Test: '0' File::Spec: '0' IO::Handle: '0' IPC::Open3: '0' Test::More: '0' lib: '0' perl: '5.006' configure_requires: ExtUtils::MakeMaker: '0' dynamic_config: 0 generated_by: 'Dist::Zilla version 6.010, CPAN::Meta::Converter version 2.150010' license: perl meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.4.html version: '1.4' name: Bio-Cluster requires: Bio::AnnotatableI: '0' Bio::Annotation::Collection: '0' Bio::Annotation::DBLink: '0' Bio::Annotation::SimpleValue: '0' Bio::DescribableI: '0' Bio::Factory::ObjectFactory: '0' Bio::Factory::SequenceStreamI: '0' Bio::IdentifiableI: '0' Bio::Root::IO: '0' Bio::Root::Root: '0' Bio::Root::RootI: '0' Bio::Seq::SeqFactory: '0' Bio::Species: '0' Bio::Variation::SNP: '0' Data::Dumper: '0' IO::File: '0' Time::HiRes: '0' XML::SAX: '0' base: '0' strict: '0' warnings: '0' resources: bugtracker: https://github.com/bioperl/bio-cluster/issues homepage: https://metacpan.org/release/Bio-Cluster repository: git://github.com/bioperl/bio-cluster.git version: 1.7.3 x_Dist_Zilla: perl: version: '5.026000' plugins: - class: Dist::Zilla::Plugin::GatherDir config: Dist::Zilla::Plugin::GatherDir: exclude_filename: [] exclude_match: [] follow_symlinks: 0 include_dotfiles: 0 prefix: '' prune_directory: [] root: . name: '@BioPerl/@Filter/GatherDir' version: '6.010' - class: Dist::Zilla::Plugin::PruneCruft name: '@BioPerl/@Filter/PruneCruft' version: '6.010' - class: Dist::Zilla::Plugin::ManifestSkip name: '@BioPerl/@Filter/ManifestSkip' version: '6.010' - class: Dist::Zilla::Plugin::MetaYAML name: '@BioPerl/@Filter/MetaYAML' version: '6.010' - class: Dist::Zilla::Plugin::License name: '@BioPerl/@Filter/License' version: '6.010' - class: Dist::Zilla::Plugin::ExtraTests name: '@BioPerl/@Filter/ExtraTests' version: '6.010' - class: Dist::Zilla::Plugin::ExecDir name: '@BioPerl/@Filter/ExecDir' version: '6.010' - class: Dist::Zilla::Plugin::ShareDir name: '@BioPerl/@Filter/ShareDir' version: '6.010' - class: Dist::Zilla::Plugin::MakeMaker config: Dist::Zilla::Role::TestRunner: default_jobs: 1 name: '@BioPerl/@Filter/MakeMaker' version: '6.010' - class: Dist::Zilla::Plugin::Manifest name: '@BioPerl/@Filter/Manifest' version: '6.010' - class: Dist::Zilla::Plugin::TestRelease name: '@BioPerl/@Filter/TestRelease' version: '6.010' - class: Dist::Zilla::Plugin::ConfirmRelease name: '@BioPerl/@Filter/ConfirmRelease' version: '6.010' - class: Dist::Zilla::Plugin::UploadToCPAN name: '@BioPerl/@Filter/UploadToCPAN' version: '6.010' - class: Dist::Zilla::Plugin::MetaConfig name: '@BioPerl/MetaConfig' version: '6.010' - class: Dist::Zilla::Plugin::MetaJSON name: '@BioPerl/MetaJSON' version: '6.010' - class: Dist::Zilla::Plugin::PkgVersion name: '@BioPerl/PkgVersion' version: '6.010' - class: Dist::Zilla::Plugin::PodSyntaxTests name: '@BioPerl/PodSyntaxTests' version: '6.010' - class: Dist::Zilla::Plugin::Test::Compile config: Dist::Zilla::Plugin::Test::Compile: bail_out_on_fail: '0' fail_on_warning: author fake_home: 0 filename: t/00-compile.t module_finder: - ':InstallModules' needs_display: 0 phase: test script_finder: - ':PerlExecFiles' skips: [] switch: [] name: '@BioPerl/Test::Compile' version: '2.057' - class: Dist::Zilla::Plugin::MojibakeTests name: '@BioPerl/MojibakeTests' version: '0.8' - class: Dist::Zilla::Plugin::AutoPrereqs name: '@BioPerl/AutoPrereqs' version: '6.010' - class: Dist::Zilla::Plugin::AutoMetaResources name: '@BioPerl/AutoMetaResources' version: '1.21' - class: Dist::Zilla::Plugin::MetaResources name: '@BioPerl/MetaResources' version: '6.010' - class: Dist::Zilla::Plugin::Encoding name: '@BioPerl/Encoding' version: '6.010' - class: Dist::Zilla::Plugin::NextRelease name: '@BioPerl/NextRelease' version: '6.010' - class: Dist::Zilla::Plugin::Git::Check config: Dist::Zilla::Plugin::Git::Check: untracked_files: die Dist::Zilla::Role::Git::DirtyFiles: allow_dirty: - Changes - dist.ini allow_dirty_match: [] changelog: Changes Dist::Zilla::Role::Git::Repo: git_version: 2.14.1 repo_root: . name: '@BioPerl/Git::Check' version: '2.042' - class: Dist::Zilla::Plugin::Git::Commit config: Dist::Zilla::Plugin::Git::Commit: add_files_in: [] commit_msg: v%v%n%n%c Dist::Zilla::Role::Git::DirtyFiles: allow_dirty: - Changes - dist.ini allow_dirty_match: [] changelog: Changes Dist::Zilla::Role::Git::Repo: git_version: 2.14.1 repo_root: . 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"is_trial" : 0 }, "version" : "6.010" } }, "x_serialization_backend" : "Cpanel::JSON::XS version 3.0239" } Makefile.PL100644000765000024 476213354321744 15773 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.010. use strict; use warnings; use 5.006; use ExtUtils::MakeMaker; my %WriteMakefileArgs = ( "ABSTRACT" => "BioPerl cluster modules", "AUTHOR" => "Allen Day , Andrew Macgregor , David Green, Hilmar Lapp , Jo-Ann Stanton, Shawn Hoon , Stan Nelson ", "CONFIGURE_REQUIRES" => { "ExtUtils::MakeMaker" => 0 }, "DISTNAME" => "Bio-Cluster", "LICENSE" => "perl", "MIN_PERL_VERSION" => "5.006", "NAME" => "Bio::Cluster", "PREREQ_PM" => { "Bio::AnnotatableI" => 0, "Bio::Annotation::Collection" => 0, "Bio::Annotation::DBLink" => 0, "Bio::Annotation::SimpleValue" => 0, "Bio::DescribableI" => 0, "Bio::Factory::ObjectFactory" => 0, "Bio::Factory::SequenceStreamI" => 0, "Bio::IdentifiableI" => 0, "Bio::Root::IO" => 0, "Bio::Root::Root" => 0, "Bio::Root::RootI" => 0, "Bio::Seq::SeqFactory" => 0, "Bio::Species" => 0, "Bio::Variation::SNP" => 0, "Data::Dumper" => 0, "IO::File" => 0, "Time::HiRes" => 0, "XML::SAX" => 0, "base" => 0, "strict" => 0, "warnings" => 0 }, "TEST_REQUIRES" => { "Bio::Root::Test" => 0, "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "lib" => 0 }, "VERSION" => "1.7.3", "test" => { "TESTS" => "t/*.t" } ); my %FallbackPrereqs = ( "Bio::AnnotatableI" => 0, "Bio::Annotation::Collection" => 0, "Bio::Annotation::DBLink" => 0, "Bio::Annotation::SimpleValue" => 0, "Bio::DescribableI" => 0, "Bio::Factory::ObjectFactory" => 0, "Bio::Factory::SequenceStreamI" => 0, "Bio::IdentifiableI" => 0, "Bio::Root::IO" => 0, "Bio::Root::Root" => 0, "Bio::Root::RootI" => 0, "Bio::Root::Test" => 0, "Bio::Seq::SeqFactory" => 0, "Bio::Species" => 0, "Bio::Variation::SNP" => 0, "Data::Dumper" => 0, "File::Spec" => 0, "IO::File" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "Time::HiRes" => 0, "XML::SAX" => 0, "base" => 0, "lib" => 0, "strict" => 0, "warnings" => 0 ); unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) { delete $WriteMakefileArgs{TEST_REQUIRES}; delete $WriteMakefileArgs{BUILD_REQUIRES}; $WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs; } delete $WriteMakefileArgs{CONFIGURE_REQUIRES} unless eval { ExtUtils::MakeMaker->VERSION(6.52) }; WriteMakefile(%WriteMakefileArgs); t000755000765000024 013354321744 14113 5ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3ClusterIO.t100644000765000024 247213354321744 16316 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t# -*-Perl-*- Test Harness script for Bioperl # $Id$ use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 12, -requires_module => 'Time::HiRes'); use_ok('Bio::ClusterIO'); use_ok('Bio::Cluster::ClusterFactory'); } SKIP: { test_skip(-tests => 8, -requires_module => 'XML::SAX'); my ($clusterio, $result,$hit,$hsp); $clusterio = Bio::ClusterIO->new('-tempfile' => 0, '-format' => 'dbsnp', '-file' => test_input_file('LittleChrY.dbsnp.xml')); $result = $clusterio->next_cluster; ok($result); is($result->observed, 'C/T'); is($result->type, 'notwithdrawn'); ok($result->seq_5); ok($result->seq_3); my @ss = $result->each_subsnp; is scalar @ss, 5; is($ss[0]->handle, 'CGAP-GAI'); is($ss[1]->handle, 'LEE'); # don't know if these were ever meant to work... cjf 3/7/07 #is($result->heterozygous, 0.208738461136818); #is($result->heterozygous_SE, 0.0260274689436777); } ################################### # ClusterFactory tests # ################################### my $fact = Bio::Cluster::ClusterFactory->new(); # auto-recognize implementation class my $clu = $fact->create_object(-display_id => 'Hs.2'); isa_ok($clu, "Bio::Cluster::UniGeneI"); $clu = $fact->create_object(-namespace => "UNIGENE"); isa_ok($clu, "Bio::Cluster::UniGeneI"); 00-compile.t100644000765000024 325713354321744 16314 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/tuse 5.006; use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::Compile 2.057 use Test::More; plan tests => 10 + ($ENV{AUTHOR_TESTING} ? 1 : 0); my @module_files = ( 'Bio/Cluster.pm', 'Bio/Cluster/ClusterFactory.pm', 'Bio/Cluster/FamilyI.pm', 'Bio/Cluster/SequenceFamily.pm', 'Bio/Cluster/UniGene.pm', 'Bio/Cluster/UniGeneI.pm', 'Bio/ClusterI.pm', 'Bio/ClusterIO.pm', 'Bio/ClusterIO/dbsnp.pm', 'Bio/ClusterIO/unigene.pm' ); # no fake home requested my @switches = ( -d 'blib' ? '-Mblib' : '-Ilib', ); use File::Spec; use IPC::Open3; use IO::Handle; open my $stdin, '<', File::Spec->devnull or die "can't open devnull: $!"; my @warnings; for my $lib (@module_files) { # see L my $stderr = IO::Handle->new; diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } $^X, @switches, '-e', "require q[$lib]")) if $ENV{PERL_COMPILE_TEST_DEBUG}; my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-e', "require q[$lib]"); binmode $stderr, ':crlf' if $^O eq 'MSWin32'; my @_warnings = <$stderr>; waitpid($pid, 0); is($?, 0, "$lib loaded ok"); shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ and not eval { +require blib; blib->VERSION('1.01') }; if (@_warnings) { warn @_warnings; push @warnings, @_warnings; } } is(scalar(@warnings), 0, 'no warnings found') or diag 'got warnings: ', ( Test::More->can('explain') ? Test::More::explain(\@warnings) : join("\n", '', @warnings) ) if $ENV{AUTHOR_TESTING}; examples000755000765000024 013354321744 15466 5ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3dbsnp.pl100644000765000024 105613354321744 17273 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/examples#!/usr/bin/perl # allenday@ucla.edu # parses a dbsnp xml file, prints some info for each refsnp and subsnp use strict; use Bio::ClusterIO; use Bio::Root::IO; use IO::File; my $file = shift @ARGV; my $io = Bio::ClusterIO->new ( -tempfile => 0, -format => 'dbsnp', -fh => IO::File->new("zcat $file |"), ); while(my $cluster = $io->next_cluster){ print $cluster->id,"\t", $cluster->observed, "\n"; foreach my $subsnp ($cluster->each_subsnp){ print "\t\t\t", $subsnp->id, "\t", $subsnp->handle, "\t", $subsnp->method, "\n"; } } SequenceFamily.t100644000765000024 243013354321744 17351 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t# -*-Perl-*- Test Harness script for Bioperl # $Id$ use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 17, -requires_module => 'Data::Stag'); use_ok('Bio::SeqIO'); use_ok('Bio::Cluster::SequenceFamily'); } my $seqio= Bio::SeqIO->new('-format' => 'swiss', '-file' => test_input_file('sequencefamily.dat')); my @mem; while(my $seq = $seqio->next_seq){ push @mem, $seq; } my $family = Bio::Cluster::SequenceFamily->new( -family_id=>"Family_1", -description=>"SomeFamily", -annotation_score=>"100", -family_score=>"50", -version=>"1.0", -members=>\@mem, ); is $family->description, "SomeFamily"; is $family->annotation_score,100; is $family->size, 5; is $family->family_id,"Family_1"; is $family->version, "1.0"; $family->add_members($mem[0]); $family->add_members($mem[1]); is $family->size, 7; is $family->cluster_score, "50"; is $family->family_score, "50"; my @members = $family->get_members(-ncbi_taxid=>9606); foreach my $mem(@members){ is $mem->species->ncbi_taxid, 9606; } @members = $family->get_members(-binomial=>"Homo sapiens"); foreach my $mem(@members){ is $mem->species->binomial, "Homo sapiens"; } $family->flush_members(); is $family->size, 0; Bio000755000765000024 013354321744 15127 5ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/libCluster.pm100644000765000024 314413354321744 17250 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio# BioPerl module for Bio::Cluster # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Cluster - BioPerl cluster modules =head1 DESCRIPTION Classes and modules here describe the basic structure for a cluster of bioperl objects. For a more complete explanation, please see the interface module L or the Bio::ClusterI-based implementations for specific examples. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon =cut package Bio::Cluster; $Bio::Cluster::VERSION = '1.7.3'; 1; Cluster-UniGene.t100644000765000024 40613354321744 17371 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t# -*-Perl-*- Test Harness script for Bioperl # $Id$ use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 2); use_ok('Bio::Cluster::UniGene'); } my $clu = Bio::Cluster::UniGene->new(); isa_ok($clu, "Bio::AnnotatableI"); data000755000765000024 013354321744 15024 5ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/tunigene.data100644000765000024 2056213354321744 17476 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t/dataID Hs.2 TITLE N-acetyltransferase 2 (arylamine N-acetyltransferase) GENE NAT2 CYTOBAND 8p22 LOCUSLINK 10 HOMOL YES EXPRESS liver ; hepatocellular carcinoma ; adenocarcinoma ; corresponding non cancerous liver tissue ; Liver ; colon ; Cell lines RESTR_EXPR liver GNM_TERMINUS S CHROMOSOME 8 STS ACC=G59899 UNISTS=137181 STS ACC=GDB:386004 UNISTS= 157141 STS ACC=WIAF-2120 UNISTS= 44576 STS ACC=G06461 UNISTS= 17088 STS ACC=GDB:310612 UNISTS= 156422 STS ACC=PMC310725P3 UNISTS= 272646 STS ACC=GDB:310613 UNISTS= 156423 STS ACC=GDB:187676 UNISTS= 155563 PROTSIM ORG=Escherischia coli; PROTGI=16129422; PROTID=ref:NP_415980.1; PCT=24.81; ALN=255 PROTSIM ORG=Homo sapiens; PROTGI=105377; PROTID=pir:B34585; PCT=100.00; ALN=290 PROTSIM ORG=Mus musculus; PROTGI=1703436; PROTID=sp:P50295; PCT=74.83; ALN=290 PROTSIM ORG=Rattus norvegicus; PROTGI=16758720; PROTID=ref:NP_446306.1; PCT=73.79; ALN=290 SCOUNT 26 SEQUENCE ACC=BX095770.1; NID=g27827877; CLONE=IMAGp998I184581_,_IMAGE:1870937; LID=1079; SEQTYPE=EST; PERIPHERAL=1 SEQUENCE ACC=AI262683.1; NID=g3870886; CLONE=IMAGE:1870937; END=3'; LID=1079; SEQTYPE=EST SEQUENCE ACC=CB161982.1; NID=g28148108; CLONE=L17N670205n1-15-F12; END=5'; LID=12542; SEQTYPE=EST; PERIPHERAL=1 SEQUENCE ACC=CB161860.1; NID=g28147986; CLONE=L17N670205n1-41-A04; END=5'; LID=12542; SEQTYPE=EST SEQUENCE ACC=AI460128.1; NID=g4313009; CLONE=IMAGE:2151449; END=3'; LID=1556; SEQTYPE=EST SEQUENCE ACC=AI733799.1; NID=g5054912; CLONE=IMAGE:1870937; END=3'; LID=1079; SEQTYPE=EST SEQUENCE ACC=AI792606.1; NID=g5340322; CLONE=IMAGE:1870937; END=5'; LID=1079; SEQTYPE=EST SEQUENCE ACC=NM_000015.1; NID=g4557782; PID=g4557783; SEQTYPE=mRNA SEQUENCE ACC=BC067218.1; NID=g45501306; PID=g45501307; SEQTYPE=mRNA SEQUENCE ACC=CR407631.1; NID=g47115198; PID=g47115199; SEQTYPE=mRNA SEQUENCE ACC=AV658623.1; NID=g9879637; CLONE=GLCFOD10; END=3'; LID=5601; SEQTYPE=EST SEQUENCE ACC=AV658656.1; NID=g9879670; CLONE=GLCFOG07; END=3'; LID=5601; SEQTYPE=EST SEQUENCE ACC=AV684197.1; NID=g10286060; CLONE=GKCFZH06; END=5'; LID=6533; SEQTYPE=EST SEQUENCE ACC=D90040.1; NID=g219411; PID=g219412; SEQTYPE=mRNA SEQUENCE ACC=AU099534.1; NID=g13550663; CLONE=HSI08034; LID=8800; SEQTYPE=EST SEQUENCE ACC=BG533459.1; NID=g13524999; CLONE=IMAGE:4072143; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44404609 SEQUENCE ACC=BG563731.1; NID=g13571383; CLONE=IMAGE:4712210; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44153506 SEQUENCE ACC=BG568400.1; NID=g13576053; CLONE=IMAGE:4716802; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44156561 SEQUENCE ACC=BG569272.1; NID=g13576925; CLONE=IMAGE:4722638; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157191 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:4722596; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44157214 SEQUENCE ACC=BG617259.1; NID=g13668630; CLONE=IMAGE:4734378; END=5'; LID=6989; SEQTYPE=EST; TRACE=44229423 SEQUENCE ACC=BG618195.1; NID=g13669566; CLONE=IMAGE:4767316; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=45338366 SEQUENCE ACC=BG204539.1; NID=g13726226; LID=8655; SEQTYPE=EST SEQUENCE ACC=BC015878.1; NID=g16198419; PID=g16198420; SEQTYPE=mRNA SEQUENCE ACC=D90042.1; NID=g219415; PID=g219416; SEQTYPE=mRNA SEQUENCE ACC=BU624903.1; NID=g23291118; CLONE=UI-H-FG1-bgl-g-02-0-UI; END=3'; LID=11914; SEQTYPE=EST; TRACE=159705553 // ID Rn.1 TITLE Transcribed sequences EXPRESS Mixed tissues STS ACC=RH128068 UNISTS=211376 SCOUNT 9 SEQUENCE ACC=AA859577.1; NID=g4230123; CLONE=UI-R-E0-bv-c-09-0-UI; END=3'; LID=1127; SEQTYPE=EST; TRACE=154346471 SEQUENCE ACC=AW251121.1; NID=g6594732; CLONE=UI-R-BJ0-adi-f-04-0-UI; END=3'; LID=2759; SEQTYPE=EST; TRACE=154371414 SEQUENCE ACC=AW252428.1; NID=g6596019; CLONE=UI-R-BJ0-adx-d-05-0-UI; END=3'; LID=2759; SEQTYPE=EST; TRACE=154373036 SEQUENCE ACC=BQ194853.1; NID=g20370404; CLONE=UI-R-CN1-cmb-f-16-0-UI; END=3'; LID=10150; SEQTYPE=EST; TRACE=154334854 SEQUENCE ACC=BU758764.1; NID=g23721624; CLONE=UI-R-FF0-cow-c-07-0-UI; END=3'; LID=11044; SEQTYPE=EST; TRACE=154339445 SEQUENCE ACC=CA510294.1; NID=g25001248; CLONE=UI-R-FS0-cqr-l-23-0-UI; END=3'; LID=12129; SEQTYPE=EST; TRACE=159666883 SEQUENCE ACC=CB613849.1; NID=g29573737; CLONE=urrg1-00170-g2; END=5'; LID=12874; SEQTYPE=EST SEQUENCE ACC=CB763094.1; NID=g29851485; CLONE=urrg1-00038-c12; END=5'; LID=12874; SEQTYPE=EST SEQUENCE ACC=CK838684.1; NID=g45188969; CLONE=UI-R-AC1-xo-a-03-0-UI; END=3'; LID=1719; SEQTYPE=EST // ID Mm.340763 TITLE Transcribed locus, strongly similar to NP_003008.1 splicing factor, arginine/serine-rich 3; splicing factor, arginine//serine-rich, 20-kD [Homo sapiens] HOMOL YES EXPRESS other ; brain ; liver ; eye ; kidney ; testis ; pituitary gland ; whole body ; colon ; muscle ; thymus CHROMOSOME 11 STS ACC=- UNISTS=3193 PROTSIM ORG=Arabidopsis thaliana; PROTGI=15236000; PROTID=ref:NP_194886.1; PCT=37.25; ALN=95 PROTSIM ORG=Caenorhabditis elegans; PROTGI=7496951; PROTID=pir:T34145; PCT=50.33; ALN=131 PROTSIM ORG=Drosophila melanogaster; PROTGI=384217; PROTID=prf:1905314A; PCT=67.29; ALN=106 PROTSIM ORG=Homo sapiens; PROTGI=139781; PROTID=sp:P23152; PCT=99.26; ALN=136 PROTSIM ORG=Mus musculus; PROTGI=111257; PROTID=pir:S14016; PCT=99.26; ALN=136 PROTSIM ORG=Rattus norvegicus; PROTGI=1168968; PROTID=sp:Q09167; PCT=48.84; ALN=83 SCOUNT 31 SEQUENCE ACC=BY050916.1; NID=g26156364; CLONE=I730062L23; END=5'; LID=12235; SEQTYPE=EST SEQUENCE ACC=BY066798.1; NID=g26170395; CLONE=I920050M24; END=5'; LID=12249; SEQTYPE=EST SEQUENCE ACC=BY297944.1; NID=g26488281; CLONE=K530357B20; END=5'; LID=12286; SEQTYPE=EST SEQUENCE ACC=BY403069.1; NID=g26632637; CLONE=I730043J07; END=3'; LID=12253; SEQTYPE=EST SEQUENCE ACC=BY417621.1; NID=g26684533; CLONE=I920028M23; END=3'; LID=4141; SEQTYPE=EST SEQUENCE ACC=BY426591.1; NID=g26701831; CLONE=I920085O07; END=3'; LID=12250; SEQTYPE=EST SEQUENCE ACC=BY448670.1; NID=g26740448; CLONE=K630031D11; END=3'; LID=2601; SEQTYPE=EST SEQUENCE ACC=BY677654.1; NID=g27066665; CLONE=K920015D15; END=3'; LID=12304; SEQTYPE=EST SEQUENCE ACC=CB947876.1; NID=g30199635; CLONE=IMAGE:30309766; END=5'; LID=12883; SEQTYPE=EST SEQUENCE ACC=CD775546.1; NID=g32434048; CLONE=UI-M-AQ0-ciz-j-19-0-UI; END=3'; LID=1947; SEQTYPE=EST SEQUENCE ACC=BX630904.1; NID=g33610776; CLONE=LIONp462B02438; END=3'; LID=14219; SEQTYPE=EST SEQUENCE ACC=CF748683.1; NID=g37645028; CLONE=IMAGE:30629174; END=5'; LID=14478; SEQTYPE=EST SEQUENCE ACC=CF750995.1; NID=g37647341; CLONE=IMAGE:30623151; END=5'; LID=14479; SEQTYPE=EST; TRACE=302787286 SEQUENCE ACC=CA587449.1; NID=g40792709; LID=12138; SEQTYPE=EST SEQUENCE ACC=CO044451.1; NID=g48584991; CLONE=IMAGE:30657728; END=3'; LID=15581; SEQTYPE=EST SEQUENCE ACC=D28619.1; NID=g618936; CLONE=86F09; LID=240; SEQTYPE=EST SEQUENCE ACC=AA474597.1; NID=g2202752; CLONE=IMAGE:805477; END=5'; LID=850; SEQTYPE=EST SEQUENCE ACC=AA498526.1; NID=g2233549; CLONE=IMAGE:889465; END=5'; LID=609; SEQTYPE=EST SEQUENCE ACC=AA638070.1; NID=g2561658; CLONE=IMAGE:1121421; END=5'; LID=916; SEQTYPE=EST; TRACE=216759053 SEQUENCE ACC=AV101859.1; NID=g5249407; CLONE=2410079M03; LID=1882; SEQTYPE=EST SEQUENCE ACC=AV113236.1; NID=g5267316; CLONE=2610020C14; LID=1884; SEQTYPE=EST SEQUENCE ACC=AI840089.1; NID=g5474302; CLONE=UI-M-AL0-abt-e-09-0-UI; END=3'; LID=1937; SEQTYPE=EST; TRACE=158440126 SEQUENCE ACC=AI843632.1; NID=g5477845; CLONE=UI-M-AO1-aen-f-09-0-UI; END=3'; LID=1944; SEQTYPE=EST; TRACE=158502493 SEQUENCE ACC=AV259282.1; NID=g6246741; CLONE=4930404D15; END=3'; LID=2547; SEQTYPE=EST SEQUENCE ACC=AV290384.1; NID=g6304415; CLONE=5133400P08; END=3'; LID=2560; SEQTYPE=EST SEQUENCE ACC=AW111788.1; NID=g6824501; CLONE=MT1455; END=3'; LID=2483; SEQTYPE=EST SEQUENCE ACC=BE333113.1; NID=g9206889; CLONE=IMAGE:3326433; END=5'; LID=544; SEQTYPE=EST; TRACE=114452409 SEQUENCE ACC=BE951610.1; NID=g10591137; CLONE=UI-M-CC0-ayc-f-08-0-UI; END=3'; LID=6769; SEQTYPE=EST; TRACE=158466712 SEQUENCE ACC=BE984495.1; NID=g10656785; CLONE=UI-M-CG0p-bgf-c-02-0-UI; END=3'; LID=6780; SEQTYPE=EST; TRACE=158541808 SEQUENCE ACC=BU525661.1; NID=g22836102; CLONE=IMAGE:6534145; END=5'; LID=11268; SEQTYPE=EST SEQUENCE ACC=BU554412.1; NID=g22904684; CLONE=IMAGE:6581716; END=5'; LID=11140; SEQTYPE=EST // ClusterI.pm100644000765000024 1014013354321744 17373 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio# # BioPerl module for Bio::ClusterI # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::ClusterI - Cluster Interface =head1 SYNOPSIS # see the implementations of this interface for details my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members = $cluster->get_members(-species=>"homo sapiens"); =head1 DESCRIPTION This interface is the basic structure for a cluster of bioperl objects. In this case it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::ClusterI; $Bio::ClusterI::VERSION = '1.7.3'; use strict; use base qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 new We don't mandate but encourage implementors to support at least the following named parameters upon object initialization. Argument Description -------- ----------- -display_id the display ID or name for the cluster -description the consensus description or name of the cluster -members the array of objects belonging to the family =cut =head2 display_id Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args : =cut sub display_id{ shift->throw_not_implemented(); } =head2 description Title : description Usage : Bio::ClusterI->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster Returns : the description string Args : Optional the description string =cut sub description{ shift->throw_not_implemented(); } =head2 size Title : size Usage : Bio::ClusterI->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family Args : =cut sub size { shift->throw_not_implemented(); } =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut sub cluster_score{ shift->throw_not_implemented(); } =head2 get_members Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria, for example : $cluster->get_members(-species => 'homo sapiens'); Will return all members if no criteria are provided. Returns : the array of members Args : =cut sub get_members { shift->throw_not_implemented(); } 1; author-mojibake.t100644000765000024 35313354321744 17502 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings qw(all); use Test::More; use Test::Mojibake; all_files_encoding_ok(); ClusterIO.pm100644000765000024 1751313354321744 17525 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio# # BioPerl module for Bio::ClusterIO.pm # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://anatomy.otago.ac.nz/meg # # You may distribute this module under the same terms as perl itself # # _history # # May 7, 2002 - changed from UniGene.pm to more generic ClusterIO.pm # by Andrew Macgregor # # April 17, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::ClusterIO - Handler for Cluster Formats =head1 SYNOPSIS #NB: This example is unigene specific use Bio::ClusterIO; $stream = Bio::ClusterIO->new('-file' => "Hs.data", '-format' => "unigene"); # note: we quote -format to keep older perl's from complaining. while ( my $in = $stream->next_cluster() ) { print $in->unigene_id() . "\n"; while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } } # Parsing errors are printed to STDERR. =head1 DESCRIPTION The ClusterIO module works with the ClusterIO format module to read various cluster formats such as NCBI UniGene. =head1 CONSTRUCTORS =head2 Bio::ClusterIO-Enew() $str = Bio::ClusterIO->new(-file => 'filename', -format=>$format); The new() class method constructs a new Bio::ClusterIO object. The returned object can be used to retrieve or print cluster objects. new() accepts the following parameters: =over 4 =item -file A file path to be opened for reading. =item -format Specify the format of the file. Supported formats include: unigene *.data UniGene build files. dbsnp *.xml dbSNP XML files If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, the main UniGene build format is assumed. The format name is case insensitive. 'UNIGENE', 'UniGene' and 'unigene' are all supported, as are dbSNP, dbsnp, and DBSNP =back =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $cluster = $str-Enext_cluster() Fetch the next cluster from the stream. =head2 TIEHANDLE(), READLINE(), PRINT() These I've left in here because they were in the SeqIO module. Feedback appreciated. There they provide the tie interface. See L for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Andrew Macgregor Email andrew@anatomy.otago.ac.nz =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::ClusterIO; $Bio::ClusterIO::VERSION = '1.7.3'; use strict; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : Bio::ClusterIO->new(-file => $filename, -format => 'format') Function: Returns a new cluster stream Returns : A Bio::ClusterIO::Handler initialised with the appropriate format Args : -file => $filename -format => format =cut my $entry = 0; sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::ClusterIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ); $format = "\L$format"; # normalize capitalization to lower case return unless( $class->_load_format_module($format) ); return "Bio::ClusterIO::$format"->new(@args); } } =head2 format Title : format Usage : $format = $stream->format() Function: Get the cluster format Returns : cluster format Args : none =cut # format() method inherited from Bio::Root::IO # _initialize is chained for all ClusterIO classes sub _initialize { my($self, @args) = @_; # initialize the IO part $self->_initialize_io(@args); } =head2 next_cluster Title : next_cluster Usage : $cluster = $stream->next_cluster() Function: Reads the next cluster object from the stream and returns it. Returns : a L compliant object Args : none =cut sub next_cluster { my ($self, $seq) = @_; $self->throw("Sorry, you cannot read from a generic Bio::ClusterIO object."); } =head2 cluster_factory Title : cluster_factory Usage : $obj->cluster_factory($newval) Function: Get/set the object factory to use for creating the cluster objects. Example : Returns : a L compliant object Args : on set, new value (a L compliant object or undef, optional) =cut sub cluster_factory{ my $self = shift; return $self->{'cluster_factory'} = shift if @_; return $self->{'cluster_factory'}; } =head2 object_factory Title : object_factory Usage : $obj->object_factory($newval) Function: This is an alias to cluster_factory with a more generic name. Example : Returns : a L compliant object Args : on set, new value (a L compliant object or undef, optional) =cut sub object_factory{ return shift->cluster_factory(@_); } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL ClusterIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::ClusterIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Function: guess format based on file suffix Example : Returns : guessed format of filename (lower case) Args : Notes : formats that _filehandle() will guess include unigene and dbsnp =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'unigene' if /\.(data)$/i; return 'dbsnp' if /\.(xml)$/i; } sub DESTROY { my $self = shift; $self->close(); } # I need some direction on these!! The module works so I haven't fiddled with them! sub TIEHANDLE { my ($class,$val) = @_; return bless {'seqio' => $val}, $class; } sub READLINE { my $self = shift; return $self->{'seqio'}->next_seq() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'seqio'}->next_seq(); return @list; } sub PRINT { my $self = shift; $self->{'seqio'}->write_seq(@_); } 1; ClusterIO-unigene.t100644000765000024 1755613354321744 17777 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t# -*-Perl-*- Test Harness script for Bioperl # $Id$ use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 73); use_ok('Bio::ClusterIO'); } my ($str, $unigene); # predeclare variables for strict $str = Bio::ClusterIO->new('-file' => test_input_file('unigene.data'), '-format' => "unigene"); ok $str, 'new Bio::ClusterIO object defined'; ok ( defined ($unigene = $str->next_cluster())); # check interface implementations to be sure isa_ok $unigene, "Bio::Cluster::UniGeneI"; isa_ok $unigene, "Bio::ClusterI"; isa_ok $unigene, "Bio::IdentifiableI"; isa_ok $unigene, "Bio::DescribableI"; # test specific instance of unigene record provided in the unigene.data file is ($unigene->unigene_id, 'Hs.2'); is ($unigene->title, 'N-acetyltransferase 2 (arylamine N-acetyltransferase)'); is ($unigene->gene, 'NAT2'); is ($unigene->cytoband,'8p22'); is ($unigene->gnm_terminus,'S'); is ($unigene->homol,'YES'); is ($unigene->restr_expr,'liver'); is ($unigene->scount,26); is (scalar @{ $unigene->locuslink }, 1); is (scalar @{ $unigene->chromosome }, 1); is (scalar @{ $unigene->express }, 7); is (scalar @{ $unigene->sts }, 8); is (scalar @{ $unigene->txmap }, 0); is (scalar @{ $unigene->protsim } , 4); is (scalar @{ $unigene->sequences },26); is ($unigene->locuslink->[0], '10'); is ($unigene->chromosome->[0], '8'); is ($unigene->express->[0], 'liver'); is ($unigene->sts->[0], 'ACC=G59899 UNISTS=137181'); is ($unigene->protsim->[0], 'ORG=Escherischia coli; PROTGI=16129422; PROTID=ref:NP_415980.1; PCT=24.81; ALN=255'); my ($seq1) = $unigene->next_seq; is ($seq1->display_id, 'BX095770'); # test recognition of species SKIP: { # TODO? why wouldn't it be available? Bug if not? Remove this skip? skip 'species not available', 'species test' unless defined $unigene->species; is $unigene->species->binomial, "Homo sapiens" ; } # test accessors of interfaces is ($seq1->namespace, "GenBank"); is ($seq1->authority, "NCBI"); is ($seq1->alphabet, "dna"); my $n = 1; # we've seen already one seq while($seq1 = $unigene->next_seq()) { $n++; } is ($n, 26); is ($unigene->size(), 26); is (scalar($unigene->get_members()), 26); is ($unigene->description, 'N-acetyltransferase 2 (arylamine N-acetyltransferase)'); is ($unigene->display_id, "Hs.2"); is ($unigene->namespace, "UniGene"); is ($unigene->authority, "NCBI"); $unigene->unigene_id('Hs.50'); is ($unigene->unigene_id, 'Hs.50') || diag('unigene_id was ' . $unigene->unigene_id); $unigene->title('title_test'); is ($unigene->title, 'title_test') || diag('title was ' . $unigene->title); $unigene->gene('gene_test'); is ($unigene->gene, 'gene_test') || diag('gene was ' . $unigene->gene); $unigene->cytoband('cytoband_test'); is ($unigene->cytoband, 'cytoband_test') || diag('cytoband was ' . $unigene->cytoband); $unigene->gnm_terminus('gnm_terminus_test'); is ($unigene->gnm_terminus, 'gnm_terminus_test') || diag('gnm_terminus was ' . $unigene->gnm_terminus); $unigene->homol('homol_test'); is ($unigene->homol, 'homol_test') || diag('homol was ' . $unigene->homol); $unigene->restr_expr('restr_expr_test'); is ($unigene->restr_expr, 'restr_expr_test') || diag('restr_expr was ' . $unigene->restr_expr); $unigene->scount('scount_test'); is ($unigene->scount, 'scount_test') || diag('scount was ' . $unigene->scount); my $seq = $unigene->next_seq; $seq = $unigene->next_seq; isa_ok ($seq, 'Bio::PrimarySeqI') || diag('expected a Bio::PrimarySeq object but got a ' . ref($seq)); my $accession = $seq->accession_number; is ($accession, 'AI262683'); my $version = $seq->seq_version(); is ($version, 1); # test the sequence parsing is working my $ac = $seq->annotation(); my $simple_ann_object; ($simple_ann_object) = $ac->get_Annotations('seqtype'); ok defined $simple_ann_object, 'annotation object defined'; is ($simple_ann_object->value(), 'EST') || diag('seqtype was ' . $simple_ann_object->value); # test PERIPHERAL, bug 1708 $seq = $unigene->next_seq; $accession = $seq->accession_number; is ($accession, 'CB161982'); my @acs = $seq->annotation->get_Annotations('peripheral'); is $acs[0]->display_text, 1; # tests not specific to unigene record provided in the unigene.data file my @locuslink_test = ( "58473", "5354" ); $unigene->locuslink(\@locuslink_test); my @locuslink_results; while (my $locuslink = $unigene->next_locuslink) { push @locuslink_results, $locuslink; } is(scalar(@locuslink_results), 2) || diag('expected locuslink to have 2 entries but it had ' . scalar(@locuslink_results)); my $locuslink = shift @locuslink_results; is( $locuslink, '58473') || diag('expected 58473 but got ' . $locuslink); my @express_test = qw( kidney heart liver spleen ); $unigene->express(\@express_test); my @express_results; while (my $tissue = $unigene->next_express) { push @express_results, $tissue; } is( scalar(@express_results), 4) || diag('expected express to have 4 entries but it had ' . scalar(@express_results)); my @chromosome_test = ( "7", "11" ); $unigene->chromosome(\@chromosome_test); my @chromosome_results; while (my $chromosome = $unigene->next_chromosome) { push @chromosome_results, $chromosome; } is( scalar(@chromosome_results), 2) || diag('expected chromosome to have 2 entries but it had ' . scalar(@chromosome_results)); my $chromosome = shift @chromosome_results; is( $chromosome, '7') || diag('expected 7 but got ' . $chromosome); my @sts_test = ( "ACC=- NAME=sts-D90276 UNISTS=37687", "ACC=G29786 NAME=SHGC-35230 UNISTS=58455" ); $unigene->sts(\@sts_test); my @sts_results; while (my $sts = $unigene->next_sts) { push @sts_results, $sts; } is(scalar(@sts_results), 2) || diag('expected sts to have 2 entries but it had ' . scalar(@sts_results)); my $sts = shift @sts_results; is($sts, 'ACC=- NAME=sts-D90276 UNISTS=37687') || diag('expected ACC=- NAME=sts-D90276 UNISTS=37687 but got ' . $sts); my @txmap_test = ("D19S425-D19S418; MARKER=sts-D90276; RHPANEL=GB4" , "D19S425-D19S418; MARKER=stSG41396; RHPANEL=GB4"); $unigene->txmap(\@txmap_test); my @txmap_results; while (my $txmap = $unigene->next_txmap) { push @txmap_results, $txmap; } is(scalar(@txmap_results), 2) || diag('expected txmap to have 2 entries but it had ' . scalar(@txmap_results)); my $txmap = shift @txmap_results; is ($txmap, 'D19S425-D19S418; MARKER=sts-D90276; RHPANEL=GB4') || diag('expected D19S425-D19S418; MARKER=sts-D90276; RHPANEL=GB4 but got ' . $txmap); my @protsim_test = ("ORG=Homo sapiens; PROTGI=107211; PROTID=pir:A40428; PCT=100; ALN=243" , "ORG=Mus musculus; PROTGI=2497288; PROTID=sp:Q61400; PCT=42; ALN=143"); $unigene->protsim(\@protsim_test); my @protsim_results; while (my $protsim = $unigene->next_protsim) { push @protsim_results, $protsim; } is (scalar(@protsim_results), 2) || diag('expected protsim to have 2 entries but it had ' . scalar(@protsim_results)); my $protsim = shift @protsim_results; is ($protsim, 'ORG=Homo sapiens; PROTGI=107211; PROTID=pir:A40428; PCT=100; ALN=243') || diag('expected ORG=Homo sapiens; PROTGI=107211; PROTID=pir:A40428; PCT=100; ALN=243 but got ' . $protsim); # do a quick test on Rn record included as the next cluster in the # test data file because it has version numbers tacked on the end of # the accession numbers in each seq line - NCBI has started doing this # now (Sept 2003). $unigene = $str->next_cluster(); $seq = $unigene->next_seq; isa_ok ($seq,'Bio::PrimarySeqI') || diag( 'expected a Bio::PrimarySeq object but got a ' . ref($seq)); $version = $seq->seq_version(); is($version, '1'); # next cluster contains a // in the title - yes NCBI did that. Nonetheless, # this should not trip up the parser: $unigene = $str->next_cluster(); ok ($unigene, 'next cluster'); # previously this would have been undef is ($unigene->unigene_id, "Mm.340763"); is ($unigene->title, 'Transcribed locus, strongly similar to NP_003008.1 splicing factor, arginine/serine-rich 3; splicing factor, arginine//serine-rich, 20-kD [Homo sapiens]'); is ($unigene->homol, 'YES'); is ($unigene->scount, 31); is (scalar($unigene->get_members()), 31); author-pod-syntax.t100644000765000024 45413354321744 20031 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests. use strict; use warnings; use Test::More; use Test::Pod 1.41; all_pod_files_ok(); sequencefamily.dat100644000765000024 11176413354321744 20742 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t/dataID MA32_HUMAN STANDARD; PRT; 282 AA. AC Q07021; DT 01-FEB-1995 (Rel. 31, Created) DT 01-FEB-1995 (Rel. 31, Last sequence update) DT 01-OCT-2000 (Rel. 40, Last annotation update) DE COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL DE PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING DE PROTEIN 1) (PRE-MRNA SPLICING FACTOR SF2, P32 SUBUNIT) (P33). GN GC1QBP OR HABP1 OR SF2P32 OR C1QBP. OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606; RN [1] RP SEQUENCE FROM N.A., AND SEQUENCE OF 74; 76-93 AND 208-216. RC TISSUE=FIBROBLAST; RX MEDLINE=94085792; PubMed=8262387; RA Honore B., Madsen P., Rasmussen H.H., Vandekerckhove J., Celis J.E., RA Leffers H.; RT "Cloning and expression of a cDNA covering the complete coding region RT of the P32 subunit of human pre-mRNA splicing factor SF2."; RL Gene 134:283-287(1993). RN [2] RP SEQUENCE OF 5-282 FROM N.A., AND SEQUENCE OF 74-114. RX MEDLINE=91309150; PubMed=1830244; RA Krainer A.R., Mayeda A., Kozak D., Binns G.; RT "Functional expression of cloned human splicing factor SF2: homology RT to RNA-binding proteins, U1 70K, and Drosophila splicing regulators."; RL Cell 66:383-394(1991). RN [3] RP SEQUENCE FROM N.A., AND PARTIAL SEQUENCE. RX MEDLINE=94253723; PubMed=8195709; RA Ghebrehiwet B., Lim B.L., Peerschke E.I., Willis A.C., Reid K.B.; RT "Isolation, cDNA cloning, and overexpression of a 33-kD cell surface RT glycoprotein that binds to the globular 'heads' of C1q."; RL J. Exp. Med. 179:1809-1821(1994). RN [4] RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS). RX MEDLINE=99199225; PubMed=10097078; RA Jiang J., Zhang Y., Krainer A.R., Xu R.-M.; RT "Crystal structure of human p32, a doughnut-shaped acidic RT mitochondrial matrix protein."; RL Proc. Natl. Acad. Sci. U.S.A. 96:3572-3577(1999). CC -!- FUNCTION: NOT KNOWN. BINDS TO THE GLOBULAR "HEADS" OF C1Q THUS CC INHIBITING C1 ACTIVATION. CC -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX. CC -!- SIMILARITY: BELONGS TO THE MAM33 FAMILY. CC -!- CAUTION: WAS ORIGINALLY (REF.1 AND REF.2) THOUGHT TO BE A PRE-MRNA CC SPLICING FACTOR THAT PLAYS A ROLE IN PREVENTING EXON SKIPPING, CC ENSURING THE ACCURACY OF SPLICING AND REGULATING ALTERNATIVE CC SPLICING. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; L04636; AAA16315.1; -. DR EMBL; M69039; AAA73055.1; -. DR EMBL; X75913; CAA53512.1; -. DR PIR; JT0762; JT0762. DR PIR; S44104; S44104. DR PDB; 1P32; 06-APR-99. DR MIM; 601269; -. KW Mitochondrion; Transit peptide; 3D-structure. FT TRANSIT 1 73 MITOCHONDRION. FT CHAIN 74 282 COMPLEMENT COMPONENT 1, Q SUBCOMPONENT FT BINDING PROTEIN. SQ SEQUENCE 282 AA; 31362 MW; 2F747FA73BB1314B CRC64; MLPLLRCVPR VLGSSVAGLR AAAPASPFRQ LLQPAPRLCT RPFGLLSVRA GSERRPGLLR PRGPCACGCG CGSLHTDGDK AFVDFLSDEI KEERKIQKHK TLPKMSGGWE LELNGTEAKL VRKVAGEKIT VTFNINNSIP PTFDGEEEPS QGQKVEEQEP ELTSTPNFVV EVIKNDDGKK ALVLDCHYPE DEVGQEDEAE SDIFSIREVS FQSTGESEWK DTNYTLNTDS LDWALYDHLM DFLADRGVDN TFADELVELS TALEHQEYIT FLEDLKSFVK SQ // ID ACON_CAEEL STANDARD; PRT; 788 AA. AC P34455; DT 01-FEB-1994 (Rel. 28, Created) DT 01-FEB-1994 (Rel. 28, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE Probable aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) DE (Citrate hydro-lyase) (Aconitase). GN F54H12.1. OS Caenorhabditis elegans. OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; OC Rhabditidae; Peloderinae; Caenorhabditis. OX NCBI_TaxID=6239; RN [1] RP SEQUENCE FROM N.A. RC STRAIN=BRISTOL N2; RX MEDLINE=94150718; PubMed=7906398; RA Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., RA Bonfield J., Burton J., Connell M., Copsey T., Cooper J., Coulson A., RA Craxton M., Dear S., Du Z., Durbin R., Favello A., Fraser A., RA Fulton L., Gardner A., Green P., Hawkins T., Hillier L., Jier M., RA Johnston L., Jones M., Kershaw J., Kirsten J., Laisster N., RA Latreille P., Lightning J., Lloyd C., Mortimore B., O'Callaghan M., RA Parsons J., Percy C., Rifken L., Roopra A., Saunders D., Shownkeen R., RA Sims M., Smaldon N., Smith A., Smith M., Sonnhammer E., Staden R., RA Sulston J., Thierry-Mieg J., Thomas K., Vaudin M., Vaughan K., RA Waterson R., Watson A., Weinstock L., Wilkinson-Sproat J., RA Wohldman P.; RT "2.2 Mb of contiguous nucleotide sequence from chromosome III of C. RT elegans."; RL Nature 368:32-38(1994). CC -!- CATALYTIC ACTIVITY: Citrate = cis-aconitate + H(2)O. CC -!- COFACTOR: ACONITASE HAS AN ACTIVE (4FE-4S) AND AN INACTIVE (3FE- CC 4S) FORMS. THE ACTIVE (4FE-4S) CLUSTER IS PART OF THE CATALYTIC CC SITE THAT INTERCONVERTS CITRATE, CIS-ACONITASE, AND ISOCITRATE (BY CC SIMILARITY). CC -!- PATHWAY: TRICARBOXYLIC ACID CYCLE. CC -!- SUBUNIT: MONOMER (BY SIMILARITY). CC -!- SUBCELLULAR LOCATION: Mitochondrial (By similarity). CC -!- SIMILARITY: BELONGS TO THE ACONITASE/IPM ISOMERASE FAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; L25599; AAA28050.1; -. DR PIR; S44831; S44831. DR HSSP; P20004; 1AMJ. DR WormPep; F54H12.1; CE00516. DR InterPro; IPR001030; Aconitase. DR InterPro; IPR000573; Aconitase_C. DR Pfam; PF00330; aconitase; 1. DR Pfam; PF00694; Aconitase_C; 1. DR PRINTS; PR00415; ACONITASE. DR ProDom; PD000511; Aconitase; 1. DR PROSITE; PS00450; ACONITASE_1; 1. DR PROSITE; PS01244; ACONITASE_2; 1. KW Hypothetical protein; Lyase; Tricarboxylic acid cycle; Iron-sulfur; KW Mitochondrion; Transit peptide; 4Fe-4S. FT TRANSIT 1 ? MITOCHONDRION (POTENTIAL). FT CHAIN ? 788 PROBABLE ACONITATE HYDRATASE. FT METAL 393 393 IRON-SULFUR (4FE-4S) (BY SIMILARITY). FT METAL 456 456 IRON-SULFUR (4FE-4S) (BY SIMILARITY). FT METAL 459 459 IRON-SULFUR (4FE-4S) (BY SIMILARITY). SQ SEQUENCE 788 AA; 85712 MW; 8861E6FC198B70D9 CRC64; MRYHFLFGSL RNHLFSFRGV IYCREKLFNC SKLSFRPSKV AISKFEPKSY LPYEKLSQTV KIVKDRLKRP LTLSEKILYG HLDQPKTQDI ERGVSYLRLR PDRVAMQDAT AQMAMLQFIS SGLPKTAVPS TIHCDHLIEA QKGGAQDLAR AKDLNKEVFN FLATAGSKYG VGFWKPGSGI IHQIILENYA FPGLLLIGTD SHTPNGGGLG GLCIGVGGAD AVDVMADIPW ELKCPKVIGI KLTGKLNGWT SAKDVILKVA DILTVKGGTG AIVEYFGPGV DSISATGMGT ICNMGAEIGA TTSVFPYNES MYKYLEATGR KEIAEEARKY KDLLTADDGA NYDQIIEINL DTLTPHVNGP FTPDLASSID KLGENAKKNG WPLDVKVSLI GSCTNSSYED MTRAASIAKQ ALDKGLKAKT IFTITPGSEQ VRATIERDGL SKIFADFGGM VLANACGPCI GQWDRQDVKK GEKNTIVTSY NRNFTGRNDA NPATHGFVTS PDITTAMAIS GRLDFNPLTD ELTAADGSKF KLQAPTGLDL PPKGYDPGED TFQAPSGSGQ VDVSPSSDRL QLLSPFDKWD GKDLEDMKIL IKVTGKCTTD HISAAGPWLK YRGHLDNISN NLFLTAINAD NGEMNKVKNQ VTGEYGAVPA TARKYKADGV RWVAIGDENY GEGSSREHAA LEPRHLGGRA IIVKSFARIH ETNLKKQGML PLTFANPADY DKIDPSDNVS IVGLSSFAPG KPLTAIFKKT NGSKVEVTLN HTFNEQQIEW FKAGSALNRM KEVFAKSK // ID 143E_HUMAN STANDARD; PRT; 255 AA. AC P42655; P29360; Q63631; DT 01-NOV-1995 (Rel. 32, Created) DT 01-NOV-1995 (Rel. 32, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE 14-3-3 protein epsilon (Mitochondrial import stimulation factor L DE subunit) (Protein kinase C inhibitor protein-1) (KCIP-1) (14-3-3E). GN YWHAE. OS Homo sapiens (Human), OS Mus musculus (Mouse), OS Rattus norvegicus (Rat), OS Bos taurus (Bovine), and OS Ovis aries (Sheep). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606, 10090, 10116, 9913, 9940; RN [1] RP SEQUENCE FROM N.A. RC SPECIES=Human; RX MEDLINE=95372385; PubMed=7644510; RA Conklin D.S., Galaktionov K., Beach D.; RT "14-3-3 proteins associate with cdc25 phosphatases."; RL Proc. Natl. Acad. Sci. U.S.A. 92:7892-7896(1995). RN [2] RP SEQUENCE FROM N.A. RC SPECIES=Human; TISSUE=Heart; RA Luk S.C.W., Lee C.Y., Waye M.M.Y.; RL Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases. RN [3] RP SEQUENCE FROM N.A. RC SPECIES=Human; RX MEDLINE=96300316; PubMed=8684458; RA Jin D.-Y., Lyu M.S., Kozak C.A., Jeang K.-T.; RT "Function of 14-3-3 proteins."; RL Nature 382:308-308(1996). RN [4] RP SEQUENCE FROM N.A. RC SPECIES=Human; TISSUE=Liver; RX MEDLINE=97011338; PubMed=8858348; RA Chong S.S., Tanigami A., Roschke A.V., Ledbetter D.H.; RT "14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on RT chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome RT region."; RL Genome Res. 6:735-741(1996). RN [5] RP SEQUENCE FROM N.A. RC SPECIES=Human; RA Tanigami A., Chong S.S., Ledbetter D.H.; RT "14-3-3 epsilon genomic sequence."; RL Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases. RN [6] RP SEQUENCE FROM N.A. RC SPECIES=Human; TISSUE=Placenta; RA Strausberg R.; RL Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases. RN [7] RP SEQUENCE FROM N.A. RC SPECIES=Rat, and Sheep; TISSUE=Pineal gland; RX MEDLINE=94296566; PubMed=8024705; RA Roseboom P.H., Weller J.L., Babila T., Aitken A., Sellers L.A., RA Moffet J.R., Namboodiri M.A., Klein D.C.; RT "Cloning and characterization of the epsilon and zeta isoforms of the RT 14-3-3 proteins."; RL DNA Cell Biol. 13:629-640(1994). RN [8] RP SEQUENCE FROM N.A. RC SPECIES=Rat; TISSUE=Liver; RX MEDLINE=95122474; PubMed=7822263; RA Alam R., Hachiya N., Sakaguchi M., Shun-Ichiro K., Iwanaga S., RA Kitajima M., Mihara K., Omura T.; RT "cDNA cloning and characterization of mitochondrial import RT stimulation factor (MSF) purified from rat liver cytosol."; RL J. Biochem. 116:416-425(1994). RN [9] RP SEQUENCE FROM N.A. RC SPECIES=Rat; TISSUE=Brain; RX MEDLINE=96280718; PubMed=8694795; RA Gao L., Gu X.B., Yu D.S., Yu R.K., Zeng G.; RT "Association of a 14-3-3 protein with CMP-NeuAc:GM1 alpha 2,3- RT sialyltransferase."; RL Biochem. Biophys. Res. Commun. 224:103-107(1996). RN [10] RP SEQUENCE FROM N.A. RC SPECIES=Mouse; STRAIN=SWISS; TISSUE=Kidney; RX MEDLINE=95269876; PubMed=7750640; RA McConnell J.E., Armstrong J.F., Bard J.B.; RT "The mouse 14-3-3 epsilon isoform, a kinase regulator whose RT expression pattern is modulated in mesenchyme and neuronal RT differentiation."; RL Dev. Biol. 169:218-228(1995). RN [11] RP SEQUENCE FROM N.A. RC SPECIES=Mouse; STRAIN=129/SV; RA Takihara Y., Irie K., Nomura M., Motaleb M., Matsumoto K., RA Shimada K.; RL Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases. RN [12] RP SEQUENCE FROM N.A. RC SPECIES=Bovine; RA Jones J.M., Niikura T., Pinke R.M., Guo W., Molday L., Leykam J., RA McConnell D.G.; RT "Expression of 14-3-3 proteins in bovine retinal photoreceptors."; RL Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases. RN [13] RP SEQUENCE OF 1-152; 165-184 AND 216-255. RC SPECIES=Sheep; TISSUE=Brain; RX MEDLINE=92283271; PubMed=1317796; RA Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.; RT "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3) RT from sheep brain. Amino acid sequence of phosphorylated forms."; RL Eur. J. Biochem. 206:453-461(1992). RN [14] RP SEQUENCE OF 1-23 AND 125-140. RC SPECIES=Sheep; TISSUE=Brain; RX MEDLINE=90345949; PubMed=2143472; RA Toker A., Ellis C.A., Sellers L.A., Aitken A.; RT "Protein kinase C inhibitor proteins. Purification from sheep brain RT and sequence similarity to lipocortins and 14-3-3 protein."; RL Eur. J. Biochem. 191:421-429(1990). CC -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE CC PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND CC STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL CC REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH CC KINASES. CC -!- SUBUNIT: HOMODIMER. CC -!- SUBCELLULAR LOCATION: CYTOPLASMIC. CC -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND CC ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO CC PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES. CC -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; U28936; AAA75301.1; -. DR EMBL; U20972; AAC50175.1; -. DR EMBL; U43399; AAC50625.1; -. DR EMBL; U43430; AAD00026.1; -. DR EMBL; U54778; AAC50710.1; -. DR EMBL; AB017103; BAA32538.1; -. DR EMBL; AB017098; BAA32538.1; JOINED. DR EMBL; AB017099; BAA32538.1; JOINED. DR EMBL; AB017100; BAA32538.1; JOINED. DR EMBL; AB017101; BAA32538.1; JOINED. DR EMBL; AB017102; BAA32538.1; JOINED. DR EMBL; BC000179; AAH00179.1; -. DR EMBL; BC001440; AAH01440.1; -. DR EMBL; M84416; AAC37659.1; -. DR EMBL; D30739; BAA06401.1; -. DR EMBL; Z19599; CAA79659.1; -. DR EMBL; U53882; AAC52676.1; -. DR EMBL; L07914; AAC37321.1; -. DR EMBL; D87663; BAA13424.1; -. DR EMBL; AF043735; AAC61927.1; -. DR PIR; S10806; S10806. DR PIR; S10807; S10807. DR HSSP; P29312; 1A38. DR MIM; 605066; -. DR MGD; MGI:894689; Ywhae. DR InterPro; IPR000308; 14-3-3. DR Pfam; PF00244; 14-3-3; 1. DR PRINTS; PR00305; 1433ZETA. DR ProDom; PD000600; 14-3-3; 1. DR SMART; SM00101; 14_3_3; 1. DR PROSITE; PS00796; 1433_1; 1. DR PROSITE; PS00797; 1433_2; 1. KW Brain; Neurone; Acetylation; Multigene family. FT MOD_RES 1 1 ACETYLATION. FT CONFLICT 73 73 K -> T (IN REF. 9). FT CONFLICT 120 120 F -> S (IN REF. 9). FT CONFLICT 123 123 K -> Y (IN REF. 9). FT CONFLICT 129 129 H -> Y (IN REF. 14). SQ SEQUENCE 255 AA; 29174 MW; 07817CCBD1F75B26 CRC64; MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW RIISSIEQKE ENKGGEDKLK MIREYRQMVE TELKLICCDI LDVLDKHLIP AANTGESKVF YYKMKGDYHR YLAEFATGND RKEAAENSLV AYKAASDIAM TELPPTHPIR LGLALNFSVF YYEILNSPDR ACRLAKAAFD DAIAELDTLS EESYKDSTLI MQLLRDNLTL WTSDMQGDGE EQNKEALQDV EDENQ // ID 143B_BOVIN STANDARD; PRT; 245 AA. AC P29358; DT 01-DEC-1992 (Rel. 24, Created) DT 01-FEB-1996 (Rel. 33, Last sequence update) DT 16-OCT-2001 (Rel. 40, Last annotation update) DE 14-3-3 protein beta/alpha (Protein kinase C inhibitor protein-1) DE (KCIP-1). GN YWHAB. OS Bos taurus (Bovine), and OS Ovis aries (Sheep). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; OC Bovidae; Bovinae; Bos. OX NCBI_TaxID=9913, 9940; RN [1] RP SEQUENCE. RC SPECIES=Bovine; RX MEDLINE=91108808; PubMed=1671102; RA Isobe T., Ichimura T., Sunaya T., Okuyama T., Takahashi N., Kuwano R., RA Takahashi Y.; RT "Distinct forms of the protein kinase-dependent activator of tyrosine RT and tryptophan hydroxylases."; RL J. Mol. Biol. 217:125-132(1991). RN [2] RP SEQUENCE OF 2-145 FROM N.A. RC SPECIES=Bovine; TISSUE=Retina; RA Jones J.M., Niikura T., Pinke R.M., Guo W., Molday L., Leykam J., RA McConnell D.G.; RT "Expression of 14-3-3 proteins in bovine retinal photoreceptors."; RL Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases. RN [3] RP SEQUENCE OF 2-83; 121-186 AND 199-241. RC SPECIES=Sheep; TISSUE=Brain; RX MEDLINE=92283271; PubMed=1317796; RA Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.; RT "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3) RT from sheep brain. Amino acid sequence of phosphorylated forms."; RL Eur. J. Biochem. 206:453-461(1992). RN [4] RP SEQUENCE OF 2-23. RC SPECIES=Sheep; TISSUE=Brain; RX MEDLINE=90345949; PubMed=2143472; RA Toker A., Ellis C.A., Sellers L.A., Aitken A.; RT "Protein kinase C inhibitor proteins. Purification from sheep brain RT and sequence similarity to lipocortins and 14-3-3 protein."; RL Eur. J. Biochem. 191:421-429(1990). RN [5] RP PHOSPHORYLATION. RC SPECIES=Sheep; RX MEDLINE=95197587; PubMed=7890696; RA Aitken A., Howell S., Jones D., Madrazo J., Patel Y.; RT "14-3-3 alpha and delta are the phosphorylated forms of RT raf-activating 14-3-3 beta and zeta. In vivo stoichiometric RT phosphorylation in brain at a Ser-Pro-Glu-Lys motif."; RL J. Biol. Chem. 270:5706-5709(1995). RN [6] RP POST-TRANSLATIONAL MODIFICATIONS. RC SPECIES=Sheep; RA Aitken A., Patel Y., Martin H., Jones D., Robinson K., Madrazo J., RA Howell S.; RT "Electrospray mass spectroscopy analysis with online trapping of RT posttranslationally modified mammalian and avian brain 14-3-3 RT isoforms."; RL J. Protein Chem. 13:463-465(1994). CC -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE CC PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND CC STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL CC REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH CC KINASES. CC -!- SUBUNIT: HOMODIMER. CC -!- SUBCELLULAR LOCATION: CYTOPLASMIC. CC -!- ALTERNATIVE PRODUCTS: TWO FORMS ARE PRODUCED BY ALTERNATIVE CC INITIATION. CC -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND CC ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO CC PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES. CC -!- PTM: ISOFORM ALPHA DIFFERS FROM ISOFORM BETA IN BEING CC PHOSPHORYLATED. CC -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; AF043736; AAC02090.1; -. DR PIR; S13467; S13467. DR PIR; S10804; S10804. DR PIR; S23179; S23179. DR HSSP; P29312; 1A38. DR InterPro; IPR000308; 14-3-3. DR Pfam; PF00244; 14-3-3; 1. DR PRINTS; PR00305; 1433ZETA. DR ProDom; PD000600; 14-3-3; 1. DR SMART; SM00101; 14_3_3; 1. DR PROSITE; PS00796; 1433_1; 1. DR PROSITE; PS00797; 1433_2; 1. KW Brain; Neurone; Phosphorylation; Acetylation; Multigene family; KW Alternative initiation. FT INIT_MET 0 0 FT CHAIN 1 245 14-3-3 PROTEIN BETA/ALPHA, LONG ISOFORM. FT CHAIN 2 245 14-3-3 PROTEIN BETA/ALPHA, SHORT ISOFORM. FT INIT_MET 2 2 FOR SHORT ISOFORM. FT MOD_RES 1 1 ACETYLATION. FT MOD_RES 2 2 ACETYLATION (IN SHORT ISOFORM). FT MOD_RES 185 185 PHOSPHORYLATION. SQ SEQUENCE 245 AA; 27950 MW; AA91C2314D99549F CRC64; TMDKSELVQK AKLAEQAERY DDMAAAMKAV TEQGHELSNE ERNLLSVAYK NVVGARRSSW RVISSIEQKT ERNEKKQQMG KEYREKIEAE LQDICNDVLQ LLDKYLIPNA TQPESKVFYL KMKGDYFRYL SEVASGDNKQ TTVSNSQQAY QEAFEISKKE MQPTHPIRLG LALNFSVFYY EILNSPEKAC SLAKTAFDEA IAELDTLNEE SYKDSTLIMQ LLRDNLTLWT SENQGDEGDA GEGEN // ID CALM_HUMAN STANDARD; PRT; 148 AA. AC P02593; P99014; P70667; Q61379; Q61380; DT 21-JUL-1986 (Rel. 01, Created) DT 21-JUL-1986 (Rel. 01, Last sequence update) DT 16-OCT-2001 (Rel. 40, Last annotation update) DE Calmodulin. GN (CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND GN (CALM3 OR CAM3 OR CAMC). OS Homo sapiens (Human), OS Mus musculus (Mouse), OS Rattus norvegicus (Rat), OS Oryctolagus cuniculus (Rabbit), OS Bos taurus (Bovine), OS Gallus gallus (Chicken), OS Anas platyrhynchos (Domestic duck), OS Xenopus laevis (African clawed frog), OS Arbacia punctulata (Punctuate sea urchin), OS Oncorhynchus sp. (Salmon), and OS Oryzias latipes (Medaka fish). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606, 10090, 10116, 9986, 9913, 9031, 8839, 8355, 7641, OX 8025, 8090; RN [1] RP SEQUENCE FROM N.A. RC SPECIES=Human; RX MEDLINE=89034207; PubMed=3182832; RA Fischer R., Koller M., Flura M., Mathews S., Strehler-Page M.A., RA Krebs J., Penniston J.T., Carafoli E., Strehler E.E.; RT "Multiple divergent mRNAs code for a single human calmodulin."; RL J. Biol. Chem. 263:17055-17062(1988). RN [2] RP SEQUENCE FROM N.A. RC SPECIES=Human; RX MEDLINE=88059053; PubMed=2445749; RA Sengupta B., Friedberg F., Detera-Wadleigh S.D.; RT "Molecular analysis of human and rat calmodulin complementary DNA RT clones. Evidence for additional active genes in these species."; RL J. Biol. Chem. 262:16663-16670(1987). RN [3] RP SEQUENCE FROM N.A. RC SPECIES=Human; RX MEDLINE=85022688; PubMed=6385987; RA Wawrzynczak E.J., Perham R.N.; RT "Isolation and nucleotide sequence of a cDNA encoding human RT calmodulin."; RL Biochem. Int. 9:177-185(1984). RN [4] RP SEQUENCE FROM N.A. RC SPECIES=Human; TISSUE=Blood; RX MEDLINE=95010144; PubMed=7925473; RA Rhyner J.A., Ottiger M., Wicki R., Greenwood T.M., Strehler E.E.; RT "Structure of the human CALM1 calmodulin gene and identification of RT two CALM1-related pseudogenes CALM1P1 and CALM1P2."; RL Eur. J. Biochem. 225:71-82(1994). RN [5] RP SEQUENCE FROM N.A. RC SPECIES=Human; TISSUE=Lymphoma; RA Kato S.; RL Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases. RN [6] RP SEQUENCE. RC SPECIES=Human; TISSUE=Brain; RX MEDLINE=82231946; PubMed=7093203; RA Sasagawa T., Ericsson L.H., Walsh K.A., Schreiber W.E., Fischer E.H., RA Titani K.; RT "Complete amino acid sequence of human brain calmodulin."; RL Biochemistry 21:2565-2569(1982). RN [7] RP SEQUENCE. RC SPECIES=Rabbit; TISSUE=Skeletal muscle; RX MEDLINE=81138220; PubMed=7202416; RA Grand R.J.A., Shenolikar S., Cohen P.; RT "The amino acid sequence of the delta subunit (calmodulin) of rabbit RT skeletal muscle phosphorylase kinase."; RL Eur. J. Biochem. 113:359-367(1981). RN [8] RP SEQUENCE. RC SPECIES=Bovine; TISSUE=Brain; RA Kasai H., Kato Y., Isobe T., Kawasaki H., Okuyama T.; RT "Determination of the complete amino acid sequence of calmodulin RT (phenylalanine-rich acidic protein II) from bovine brain."; RL Biomed. Res. 1:248-264(1980). RN [9] RP SEQUENCE. RC SPECIES=Bovine; TISSUE=Brain; RX MEDLINE=80094551; PubMed=7356670; RA Watterson D.M., Sharief F., Vanaman T.C.; RT "The complete amino acid sequence of the Ca2+-dependent modulator RT protein (calmodulin) of bovine brain."; RL J. Biol. Chem. 255:962-975(1980). RN [10] RP SEQUENCE. RC SPECIES=Bovine; TISSUE=Uterus; RA Grand R.J.A., Perry S.V.; RT "The amino acid sequence of the troponin C-like protein (modulator RT protein) from bovine uterus."; RL FEBS Lett. 92:137-142(1978). RN [11] RP SEQUENCE OF 38-60. RC SPECIES=Bovine; RX MEDLINE=89064822; PubMed=3058479; RA Pribilla I., Krueger H., Buchner K., Otto H., Schiebler W., RA Tripier D., Hucho F.; RT "Heat-resistant inhibitors of protein kinase C from bovine brain."; RL Eur. J. Biochem. 177:657-664(1988). RN [12] RP SEQUENCE FROM N.A. RC SPECIES=Mouse; RX MEDLINE=88257100; PubMed=3384819; RA Bender P.K., Dedman J.R., Emerson C.P.; RT "The abundance of calmodulin mRNAs is regulated in phosphorylase RT kinase-deficient skeletal muscle."; RL J. Biol. Chem. 263:9733-9737(1988). RN [13] RP SEQUENCE FROM N.A. RC SPECIES=Mouse; RX MEDLINE=90006775; PubMed=2551780; RA Danchin A., Sezer O., Glaser P., Chalon P., Caput D.; RT "Cloning and expression of mouse-brain calmodulin as an activator of RT Bordetella pertussis adenylate cyclase in Escherichia coli."; RL Gene 80:145-149(1989). RN [14] RP SEQUENCE FROM N.A. RC SPECIES=Mouse; STRAIN=BALB/C; TISSUE=Brain; RA Kato K.; RT "A collection of cDNA clones with specific expression patterns in RT mouse brain."; RL Eur. J. Neurosci. 2:704-711(1991). RN [15] RP SEQUENCE. RC SPECIES=Rat; TISSUE=Testis; RX MEDLINE=78066877; PubMed=201628; RA Dedman J.R., Jackson R.L., Schreiber W.E., Means A.R.; RT "Sequence homology of the Ca2+-dependent regulator of cyclic RT nucleotide phosphodiesterase from rat testis with other Ca2+-binding RT proteins."; RL J. Biol. Chem. 253:343-346(1978). RN [16] RP SEQUENCE FROM N.A. RC SPECIES=Rat; TISSUE=Brain; RX MEDLINE=87246077; PubMed=2885164; RA Sherbany A.A., Parent A.S., Brosius J.; RT "Rat calmodulin cDNA."; RL DNA 6:267-272(1987). RN [17] RP SEQUENCE FROM N.A. RC SPECIES=Rat; TISSUE=Brain; RX MEDLINE=87226204; PubMed=3035194; RA Nojima H., Hirofumi S.; RT "Structure of a gene for rat calmodulin."; RL J. Mol. Biol. 193:439-445(1987). RN [18] RP SEQUENCE FROM N.A. RC SPECIES=Rat; RX MEDLINE=87257889; PubMed=3037336; RA Nojima H., Kishi K., Sokabe H.; RT "Multiple calmodulin mRNA species are derived from two distinct RT genes."; RL Mol. Cell. Biol. 7:1873-1880(1987). RN [19] RP SEQUENCE FROM N.A. RC SPECIES=Rat; STRAIN=SHR; RX MEDLINE=89362474; PubMed=2527998; RA Nojima H.; RT "Structural organization of multiple rat calmodulin genes."; RL J. Mol. Biol. 208:269-282(1989). RN [20] RP SEQUENCE FROM N.A. RC SPECIES=Chicken; RX MEDLINE=84008199; PubMed=6137485; RA Putkey J.A., Ts'Ui K.F., Tanaka T., Lagace L., Stein J.P., Lai E.C., RA Means A.R.; RT "Chicken calmodulin genes. A species comparison of cDNA sequences and RT isolation of a genomic clone."; RL J. Biol. Chem. 258:11864-11870(1983). RN [21] RP SEQUENCE FROM N.A. RC SPECIES=Chicken; RX MEDLINE=85104969; PubMed=2981850; RA Simmen R.C.M., Tanaka T., Ts'Ui K.F., Putkey J.A., Scott M.J., RA Lai E.C., Means A.R.; RT "The structural organization of the chicken calmodulin gene."; RL J. Biol. Chem. 260:907-912(1985). RN [22] RP ERRATUM. RC SPECIES=Chicken; RA Simmen R.C.M., Tanaka T., Ts'Ui K.F., Putkey J.A., Scott M.J., RA Lai E.C., Means A.R.; RL J. Biol. Chem. 262:4928-4929(1987). RN [23] RP SEQUENCE FROM N.A. RC SPECIES=Chicken; RA Iida Y.; RT "cDNA sequences and molecular evolution of calmodulin genes of RT chicken and eel."; RL Bull. Chem. Soc. Jpn. 57:2667-2668(1984). RN [24] RP SEQUENCE FROM N.A. RC SPECIES=A.platyrhynchos; RX MEDLINE=93287810; PubMed=8389959; RA Kimura N., Kurosawa N., Kondo K., Tsukada Y.; RT "Molecular cloning of the kainate-binding protein and calmodulin RT genes which are induced by an imprinting stimulus in ducklings."; RL Brain Res. Mol. Brain Res. 17:351-355(1993). RN [25] RP SEQUENCE FROM N.A. RC SPECIES=X.laevis; RX MEDLINE=84191128; PubMed=6325880; RA Chien Y.-H., Dawid I.B.; RT "Isolation and characterization of calmodulin genes from Xenopus RT laevis."; RL Mol. Cell. Biol. 4:507-513(1984). RN [26] RP SEQUENCE OF 1-141 FROM N.A. RC SPECIES=A.punctulata; RX MEDLINE=88172463; PubMed=3351921; RA Hardy D.O., Bender P.K., Kretsinger R.H.; RT "Two calmodulin genes are expressed in Arbacia punctulata. An ancient RT gene duplication is indicated."; RL J. Mol. Biol. 199:223-227(1988). RN [27] RP SEQUENCE. RC SPECIES=Salmon; RA Yazawa M., Toda H., Yagi Y.; RT "Amino acid sequence of salmon calmodulin."; RL Seikagaku 57:1037-1037(1985). RN [28] RP SEQUENCE FROM N.A. RC SPECIES=O.latipes; RX MEDLINE=93012998; PubMed=1398109; RA Matsuo K., Sato K., Ikeshima H., Shimoda K., Takano T.; RT "Four synonymous genes encode calmodulin in the teleost fish, medaka RT (Oryzias latipes): conservation of the multigene one-protein RT principle."; RL Gene 119:279-281(1992). RN [29] RP SEQUENCE OF 1-27, AND UBIQUITYLATION OF LYS-21. RC SPECIES=Bovine; RX MEDLINE=98380241; PubMed=9716384; RA Laub M., Steppuhn J.A., Blueggel M., Immler D., Meyer H.E., RA Jennissen H.P.; RT "Modulation of calmodulin function by ubiquitin-calmodulin ligase and RT identification of the responsible ubiquitylation site in vertebrate RT calmodulin."; RL Eur. J. Biochem. 255:422-431(1998). RN [30] RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS). RC SPECIES=Rat; RX MEDLINE=85188323; PubMed=3990807; RA Babu Y.S., Sack J.S., Greenhough T.J., Bugg C.E., Means A.R., RA Cook W.J.; RT "Three-dimensional structure of calmodulin."; RL Nature 315:37-40(1985). RN [31] RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS). RC SPECIES=Rat; RX MEDLINE=89110997; PubMed=3145979; RA Babu Y.S., Bugg C.E., Cook W.J.; RT "Structure of calmodulin refined at 2.2-A resolution."; RL J. Mol. Biol. 204:191-204(1988). RN [32] RP X-RAY CRYSTALLOGRAPHY (2 ANGSTROMS). RC SPECIES=Bovine; RX MEDLINE=98104088; PubMed=9438860; RA Wall M.E., Clarage J.B., Phillips G.N.; RT "Motions of calmodulin characterized using both Bragg and diffuse RT X-ray scattering."; RL Structure 5:1599-1612(1997). RN [33] RP STRUCTURE BY NMR OF 76-148. RX MEDLINE=94085641; PubMed=8262263; RA Finn B.E., Drakenberg T., Forsen S.; RT "The structure of apo-calmodulin. A 1H NMR examination of the RT carboxy-terminal domain."; RL FEBS Lett. 336:368-374(1993). RN [34] RP STRUCTURE BY NMR OF 76-148. RX MEDLINE=96018615; PubMed=7552749; RA Finn B.E., Evenas J., Drakenberg T., Waltho J.P., Thulin E., RA Forsen S.; RT "Calcium-induced structural changes and domain autonomy in RT calmodulin."; RL Nat. Struct. Biol. 2:777-783(1995). RN [35] RP STRUCTURE BY NMR. RX MEDLINE=96018613; PubMed=7552747; RA Zhang M., Tanaka T., Ikura M.; RT "Calcium-induced conformational transition revealed by the solution RT structure of apo calmodulin."; RL Nat. Struct. Biol. 2:758-767(1995). RN [36] RP STRUCTURE BY NMR. RX MEDLINE=96018614; PubMed=7552748; RA Kuboniwa H., Tjandra N., Grzesiek S., Ren H., Klee C.B., Bax A.; RT "Solution structure of calcium-free calmodulin."; RL Nat. Struct. Biol. 2:768-776(1995). RN [37] RP STRUCTURE BY NMR. RX MEDLINE=98179557; PubMed=9514729; RA Osawa M., Swindells M.B., Tanikawa J., Tanaka T., Mase T., Furuya T., RA Ikura M.; RT "Solution structure of calmodulin-W-7 complex: the basis of diversity RT in molecular recognition."; RL J. Mol. Biol. 276:165-176(1998). RN [38] RP STRUCTURE BY NMR. RX MEDLINE=99425120; PubMed=10493800; RA Elshorst B., Hennig M., Foersterling H., Diener A., Maurer M., RA Schulte P., Schwalbe H., Griesinger C., Krebs J., Schmid H., RA Vorherr T., Carafoli E.; RT "NMR solution structure of a complex of calmodulin with a binding RT peptide of the Ca(2+) pump."; RL Biochemistry 38:12320-12332(1999). CC -!- FUNCTION: CALMODULIN MEDIATES THE CONTROL OF A LARGE NUMBER OF CC ENZYMES BY CA(++). AMONG THE ENZYMES TO BE STIMULATED BY THE CC CALMODULIN-CA(++) COMPLEX ARE A NUMBER OF PROTEIN KINASES AND CC PHOSPHATASES. CC -!- PTM: UBIQUITYLATION STRONGLY DECREASES THE ACTIVITY. CC -!- MISCELLANEOUS: THIS PROTEIN HAS FOUR FUNCTIONAL CALCIUM-BINDING CC SITES. CC -!- SIMILARITY: TO OTHER EF-HAND CALCIUM BINDING PROTEINS. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; L00101; AAA48653.1; -. DR EMBL; L00096; AAA48653.1; JOINED. DR EMBL; L00097; AAA48653.1; JOINED. DR EMBL; L00098; AAA48653.1; JOINED. DR EMBL; L00099; AAA48653.1; JOINED. DR EMBL; L00100; AAA48653.1; JOINED. DR EMBL; M16659; AAA40864.1; -. DR EMBL; M27319; AAA35635.1; -. DR EMBL; U12022; AAB60644.1; -. DR EMBL; U11886; AAB60644.1; JOINED. DR EMBL; D45887; BAA08302.1; -. DR EMBL; X13817; CAA32050.1; -. DR EMBL; J04046; AAA51918.1; -. DR EMBL; M19311; AAA35641.1; -. DR EMBL; M19312; AAA40862.1; -. DR EMBL; M17069; AAA40863.1; -. DR EMBL; X13933; CAA32120.1; -. DR EMBL; X13931; CAA32119.1; -. DR EMBL; X13932; CAA32119.1; JOINED. DR EMBL; X05117; CAA32119.1; JOINED. DR EMBL; X13833; CAA32062.1; -. DR EMBL; X13834; CAA32062.1; JOINED. DR EMBL; X13835; CAA32062.1; JOINED. DR EMBL; X14265; CAA32478.1; -. DR EMBL; D83350; BAA11896.1; -. DR EMBL; M36167; AAA48650.1; -. DR EMBL; K01944; AAA49668.1; -. DR EMBL; K01945; AAA49669.1; -. DR EMBL; D10363; BAA01195.1; -. DR EMBL; M19380; AAA66181.1; -. DR EMBL; M19381; AAA66182.1; -. DR EMBL; L31642; AAA65934.1; -. DR EMBL; M27844; AAA37365.1; -. DR EMBL; X61432; CAA43674.1; -. DR PIR; S13159; MCHU. DR PIR; JK0013; MCON. DR PIR; A90719; MCBO. DR PIR; A91104; MCRB. DR PIR; S03206; MCRT. DR PIR; A92394; MCCH. DR PIR; S02690; S02690. DR PIR; A60781; A60781. DR PIR; JC1305; JC1305. DR PDB; 2CLN; 15-OCT-94. DR PDB; 3CLN; 09-JAN-89. DR PDB; 1TRC; 15-OCT-91. DR PDB; 1AK8; 17-SEP-97. DR PDB; 1CDL; 31-AUG-94. DR PDB; 1CDM; 31-AUG-94. DR PDB; 1CFC; 07-DEC-95. DR PDB; 1CFD; 07-DEC-95. DR PDB; 1CLL; 31-OCT-93. DR PDB; 1CM1; 04-MAR-98. DR PDB; 1CM4; 04-MAR-98. DR PDB; 1CMF; 07-DEC-95. DR PDB; 1CMG; 07-DEC-95. DR PDB; 1CTR; 20-DEC-94. DR PDB; 1DEG; 31-MAY-94. DR PDB; 1DMO; 01-AUG-96. DR PDB; 1LIN; 08-MAR-96. DR PDB; 1AJI; 17-SEP-97. DR PDB; 1A29; 16-SEP-98. DR PDB; 1MUX; 25-NOV-98. DR PDB; 1CFF; 24-SEP-91. DR SWISS-2DPAGE; P99014; MOUSE. DR Aarhus/Ghent-2DPAGE; 9048; IEF. DR MIM; 114180; -. DR MIM; 114182; -. DR MIM; 114183; -. DR MGD; MGI:88251; Calm. DR MGD; MGI:103250; Calm2. DR MGD; MGI:103249; Calm3. DR InterPro; IPR002048; EF-hand. DR Pfam; PF00036; efhand; 4. DR SMART; SM00054; EFh; 4. DR PROSITE; PS00018; EF_HAND; 4. KW Calcium-binding; Duplication; Methylation; Acetylation; KW 3D-structure. FT INIT_MET 0 0 FT MOD_RES 1 1 ACETYLATION. FT MOD_RES 115 115 METHYLATION (TRI-) (IN CHICKEN). FT CA_BIND 20 31 EF-HAND 1. FT CA_BIND 56 67 EF-HAND 2. FT CA_BIND 93 104 EF-HAND 3. FT CA_BIND 129 140 EF-HAND 4. FT BINDING 21 21 UBIQUITIN (MULTI-). FT CONFLICT 25 25 G -> N (IN REF. 12; AAA66182). FT HELIX 5 19 FT TURN 21 22 FT STRAND 26 27 FT HELIX 29 37 FT TURN 38 40 FT HELIX 45 55 FT TURN 57 58 FT STRAND 63 64 FT HELIX 65 92 FT TURN 94 95 FT STRAND 100 100 FT HELIX 102 111 FT TURN 112 113 FT HELIX 118 128 FT STRAND 136 136 FT HELIX 138 146 SQ SEQUENCE 148 AA; 16706 MW; 464B8A287475A1CA CRC64; ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK // Cluster000755000765000024 013354321744 16550 5ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/BioUniGene.pm100644000765000024 10434613354321744 20650 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/Cluster# # BioPerl module for Bio::Cluster::UniGene.pm # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://meg.otago.ac.nz/ # # You may distribute this module under the same terms as perl itself # # _history # April 17, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::Cluster::UniGene - UniGene object =head1 SYNOPSIS use Bio::Cluster::UniGene; use Bio::ClusterIO; $stream = Bio::ClusterIO->new('-file' => "Hs.data", '-format' => "unigene"); # note: we quote -format to keep older perl's from complaining. while ( my $in = $stream->next_cluster() ) { print $in->unigene_id() . "\n"; while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } } =head1 DESCRIPTION This UniGene object implements the L interface for the representation if UniGene clusters in Bioperl. It is returned by the L parser for unigene format and contains all the data associated with one UniGene record. This class implements several interfaces and hence can be used wherever instances of such interfaces are expected. In particular, the interfaces are L as the base interface for all cluster representations, and in addition L and L. The following lists the UniGene specific methods that are available (see below for details). Be aware next_XXX iterators take a snapshot of the array property when they are first called, and this snapshot is not reset until the iterator is exhausted. Hence, once called you need to exhaust the iterator to see any changes that have been made to the property in the meantime. You will usually want to use the non-iterator equivalents and loop over the elements yourself. new() - standard new call unigene_id() - set/get unigene_id title() - set/get title (description) gene() - set/get gene cytoband() - set/get cytoband mgi() - set/get mgi locuslink() - set/get locuslink homol() - set/get homologene gnm_terminus() - set/get gnm_terminus scount() - set/get scount express() - set/get express, currently takes/returns a reference to an array of expressed tissues next_express() - returns the next tissue expression from the expressed tissue array chromosome() - set/get chromosome, currently takes/returns a reference to an array of chromosome lines next_chromosome() - returns the next chromosome line from the array of chromosome lines sts() - set/get sts, currently takes/returns a reference to an array of sts lines next_sts() - returns the next sts line from the array of sts lines txmap() - set/get txmap, currently takes/returns a reference to an array of txmap lines next_txmap() - returns the next txmap line from the array of txmap lines protsim() - set/get protsim, currently takes/returns a reference to an array of protsim lines next_protsim() - returns the next protsim line from the array of protsim lines sequences() - set/get sequence, currently takes/returns a reference to an array of references to seq info next_seq() - returns a Seq object that currently only contains an accession number =head1 Implemented Interfaces This class implementes the following interfaces. =over 4 =item Bio::Cluster::UniGeneI This includes implementing Bio::ClusterI. =item Bio::IdentifiableI =item Bio::DescribableI =item Bio::AnnotatableI =item Bio::Factory::SequenceStreamI =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Andrew Macgregor Email andrew at cbbc.murdoch.edu.au =head1 CONTRIBUTORS Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Cluster::UniGene; $Bio::Cluster::UniGene::VERSION = '1.7.3'; use strict; use Bio::Annotation::Collection; use Bio::Annotation::DBLink; use Bio::Annotation::SimpleValue; use Bio::Species; use Bio::Seq::SeqFactory; use base qw(Bio::Root::Root Bio::Cluster::UniGeneI Bio::IdentifiableI Bio::DescribableI Bio::AnnotatableI Bio::Factory::SequenceStreamI); my %species_map = ( 'Aga' => "Anopheles gambiae", 'Ame' => "Apis mellifera", 'At' => "Arabidopsis thaliana", 'Bmo' => "Bombyx mori", 'Bt' => "Bos taurus", 'Cel' => "Caenorhabditis elegans", 'Cfa' => "Canine familiaris", 'Cin' => "Ciona intestinalis", 'Cre' => "Chlamydomonas reinhardtii", 'Csa' => "Ciona savignyi", 'Csi' => "Citrus sinensis", 'Ddi' => "Dictyostelium discoideum", 'Dr' => "Danio rerio", 'Dm' => "Drosophila melanogaster", 'Gga' => "Gallus gallus", 'Gma' => "Glycine max", 'Han' => "Helianthus annus", 'Hs' => "Homo sapiens", 'Hma' => "Hydra magnipapillata", 'Hv' => "Hordeum vulgare", 'Lco' => "Lotus corniculatus", 'Les' => "Lycopersicon esculentum", 'Lsa' => "Lactuca sativa", 'Mdo' => "Malus x domestica", 'Mgr' => "Magnaporthe grisea", 'Mm' => "Mus musculus", 'Mtr' => "Medicago truncatula", 'Ncr' => "Neurospora crassa", 'Oar' => "Ovis aries", 'Omy' => "Oncorhynchus mykiss", 'Os' => "Oryza sativa", 'Ola' => "Oryzias latipes", 'Ppa' => "Physcomitrella patens", 'Pta' => "Pinus taeda", 'Ptp' => "Populus tremula x Populus tremuloides", 'Rn' => "Rattus norvegicus", 'Sbi' => "Sorghum bicolor", 'Sma' => "Schistosoma mansoni", 'Sof' => "Saccharum officinarum", 'Spu' => "Strongylocentrotus purpuratus", 'Ssa' => "Salmo salar", 'Ssc' => "Sus scrofa", 'Str' => "Xenopus tropicalis", 'Stu' => "Solanum tuberosum", 'Ta' => "Triticum aestivum", 'Tgo' => "Toxoplasma gondii", 'Tru' => "Takifugu rubripes", 'Vvi' => "Vitis vinifera", 'Xl' => "Xenopus laevis", 'Zm' => "Zea mays", ); =head2 new Title : new Usage : used by ClusterIO Returns : a new Bio::Cluster::Unigene object =cut sub new { # standard new call.. my($caller,@args) = @_; my $self = $caller->SUPER::new(@args); my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) = $self->_rearrange([qw(UNIGENE_ID DESCRIPTION MEMBERS SIZE SPECIES DISPLAY_ID OBJECT_ID NAMESPACE AUTHORITY VERSION SEQFACTORY )], @args); $self->{'_alphabet'} = 'dna'; $self->unigene_id($ugid) if $ugid; $self->description($desc) if $desc; $self->sequences($mems) if $mems; $self->size($size) if defined($size); $self->display_id($dispid) if $dispid; # overwrites ugid $self->object_id($id) if $id; # overwrites dispid $self->namespace($ns || 'UniGene'); $self->authority($auth || 'NCBI'); $self->version($v) if defined($v); if( ! defined $seqfact ) { $seqfact = Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq'); } $self->sequence_factory($seqfact); if( (! $species) && (defined $self->unigene_id() && $self->unigene_id() =~ /^([A-Za-z]+)\.[0-9]/)) { # try set a default one depending on the ID $species = $species_map{$1}; } $self->species($species); return $self; } =head1 L methods =cut =head2 unigene_id Title : unigene_id Usage : unigene_id(); Function: Returns the unigene_id associated with the object. Example : $id = $unigene->unigene_id or $unigene->unigene_id($id) Returns : A string Args : None or an id =cut sub unigene_id { my ($obj,$value) = @_; if( defined $value) { $obj->{'unigene_id'} = $value; } return $obj->{'unigene_id'}; } =head2 title Title : title Usage : title(); Function: Returns the title associated with the object. Example : $title = $unigene->title or $unigene->title($title) Returns : A string Args : None or a title =cut sub title { my ($obj,$value) = @_; if( defined $value) { $obj->{'title'} = $value; } return $obj->{'title'}; } =head2 gene Title : gene Usage : gene(); Function: Returns the gene associated with the object. Example : $gene = $unigene->gene or $unigene->gene($gene) Returns : A string Args : None or a gene =cut sub gene { my $self = shift; return $self->_annotation_value('gene_name', @_); } =head2 cytoband Title : cytoband Usage : cytoband(); Function: Returns the cytoband associated with the object. Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband) Returns : A string Args : None or a cytoband =cut sub cytoband { my $self = shift; return $self->_annotation_value('cyto_band', @_); } =head2 mgi Title : mgi Usage : mgi(); Function: Returns the mgi associated with the object. Example : $mgi = $unigene->mgi or $unigene->mgi($mgi) Returns : A string Args : None or a mgi =cut sub mgi { my $self = shift; my $acc; if(@_) { # purge first $self->_remove_dblink('dblink','MGI'); # then add if a valid value is present if($acc = shift) { $self->_annotation_dblink('dblink','MGI',$acc); } } else { ($acc) = $self->_annotation_dblink('dblink','MGI'); } return $acc; } =head2 locuslink Title : locuslink Usage : locuslink(); Function: Returns or stores a reference to an array containing locuslink data. Returns : An array reference Args : None or an array reference =cut sub locuslink { my ($self,$ll) = @_; if($ll) { # purge first $self->_remove_dblink('dblink','LocusLink'); # then add as many accessions as are present foreach my $acc (@$ll) { $self->_annotation_dblink('dblink','LocusLink',$acc); } } else { my @accs = $self->_annotation_dblink('dblink','LocusLink'); $ll = [@accs]; } return $ll; } =head2 homol Title : homol Usage : homol(); Function: Returns the homol entry associated with the object. Example : $homol = $unigene->homol or $unigene->homol($homol) Returns : A string Args : None or a homol entry =cut sub homol { my $self = shift; return $self->_annotation_value('homol', @_); } =head2 restr_expr Title : restr_expr Usage : restr_expr(); Function: Returns the restr_expr entry associated with the object. Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr) Returns : A string Args : None or a restr_expr entry =cut sub restr_expr { my $self = shift; return $self->_annotation_value('restr_expr', @_); } =head2 gnm_terminus Title : gnm_terminus Usage : gnm_terminus(); Function: Returns the gnm_terminus associated with the object. Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus) Returns : A string Args : None or a gnm_terminus =cut sub gnm_terminus { my $self = shift; return $self->_annotation_value('gnm_terminus', @_); } =head2 scount Title : scount Usage : scount(); Function: Returns the scount associated with the object. Example : $scount = $unigene->scount or $unigene->scount($scount) Returns : A string Args : None or a scount =cut sub scount { my ($obj,$value) = @_; if( defined $value) { $obj->{'scount'} = $value; } elsif((! defined($obj->{'scount'})) && defined($obj->sequences())) { $obj->{'scount'} = $obj->size(); } return $obj->{'scount'}; } =head2 express Title : express Usage : express(); Function: Returns or stores a reference to an array containing tissue expression data Returns : An array reference Args : None or an array reference =cut sub express { my $self = shift; return $self->_annotation_value_ary('expressed',@_); } =head2 chromosome Title : chromosome Usage : chromosome(); Function: Returns or stores a reference to an array containing chromosome lines Returns : An array reference Args : None or an array reference =cut sub chromosome { my $self = shift; return $self->_annotation_value_ary('chromosome',@_); } =head2 sts Title : sts Usage : sts(); Function: Returns or stores a reference to an array containing sts lines Returns : An array reference Args : None or an array reference =cut sub sts { my $self = shift; return $self->_annotation_value_ary('sts',@_); } =head2 txmap Title : txmap Usage : txmap(); Function: Returns or stores a reference to an array containing txmap lines Returns : An array reference Args : None or an array reference =cut sub txmap { my $self = shift; return $self->_annotation_value_ary('txmap',@_); } =head2 protsim Title : protsim Usage : protsim(); Function: Returns or stores a reference to an array containing protsim lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub protsim { my $self = shift; return $self->_annotation_value_ary('protsim',@_); } =head2 sequences Title : sequences Usage : sequences(); Function: Returns or stores a reference to an array containing sequence data. This is mostly reserved for ClusterIO parsers. You should use get_members() for get and add_member()/remove_members() for set. Returns : An array reference, or undef Args : None or an array reference or undef =cut sub sequences { my $self = shift; return $self->{'members'} = shift if @_; return $self->{'members'}; } =head2 species Title : species Usage : $obj->species($newval) Function: Get/set the species object for this Unigene cluster. Example : Returns : value of species (a L object) Args : on set, new value (a L object or the binomial name, or undef, optional) =cut sub species{ my $self = shift; if(@_) { my $species = shift; if($species && (! ref($species))) { my @class = reverse(split(' ',$species)); $species = Bio::Species->new(-classification => \@class); } return $self->{'species'} = $species; } return $self->{'species'}; } =head1 L methods =cut =head2 display_id Title : display_id Usage : Function: Get/set the display name or identifier for the cluster This is aliased to unigene_id(). Returns : a string Args : optional, on set the display ID ( a string) =cut sub display_id{ return shift->unigene_id(@_); } =head2 description Title : description Usage : Bio::ClusterI->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster This is aliased to title(). Returns : the description string Args : Optional the description string =cut sub description{ return shift->title(@_); } =head2 size Title : size Usage : Bio::ClusterI->size(); Function: get for the size of the family, calculated from the number of members This is aliased to scount(). Returns : the size of the cluster Args : =cut sub size { my $self = shift; # hard-wiring the size is allowed if there are no sequences return $self->scount(@_) unless defined($self->sequences()); # but we can't change the number of members through this method my $n = scalar(@{$self->sequences()}); if(@_ && ($n != $_[0])) { $self->throw("Cannot change cluster size using size() from $n to ". $_[0]); } return $n; } =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. For UniGene clusters, there really is no cluster score that would come with the data. However, we provide an implementation here so that you can score UniGene clusters if you want to. Returns : a number Args : optionally, on set a number =cut sub cluster_score{ my $self = shift; return $self->{'cluster_score'} = shift if @_; return $self->{'cluster_score'}; } =head2 get_members Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria Will return all members if no criteria are provided. At this time this implementation does not support specifying criteria and will always return all members. Returns : the array of members Args : =cut sub get_members { my $self = shift; my $mems = $self->sequences() || []; # already objects? if(@$mems && (ref($mems->[0]) eq "HASH")) { # nope, we need to build the object list from scratch my @memlist = (); while(my $seq = $self->next_seq()) { push(@memlist, $seq); } # we cache this array of objects as the new member list $mems = \@memlist; $self->sequences($mems); } # done return @$mems; } =head1 Annotatable view at the object properties =cut =head2 annotation Title : annotation Usage : $obj->annotation($newval) Function: Get/set the L object for this UniGene cluster. Many attributes of this class are actually stored within the annotation collection object as L compliant objects, so you can conveniently access them through the same interface as you would e.g. access L annotation properties. If you call this method in set mode and replace the annotation collection with another one you should know exactly what you are doing. Example : Returns : a L compliant object Args : on set, new value (a L compliant object or undef, optional) =cut sub annotation{ my $self = shift; if(@_) { return $self->{'annotation'} = shift; } elsif(! exists($self->{'annotation'})) { $self->{'annotation'} = Bio::Annotation::Collection->new(); } return $self->{'annotation'}; } =head1 Implementation specific methods These are mostly for adding/removing to array properties, and for methods with special functionality. =cut =head2 add_member Title : add_member Usage : Function: Adds a member object to the list of members. Example : Returns : TRUE if the new member was successfully added, and FALSE otherwise. Args : The member to add. =cut sub add_member{ my ($self,@mems) = @_; my $memlist = $self->{'members'} || []; # this is an object interface; is the member list already objects? if(@$memlist && (ref($memlist->[0]) eq "HASH")) { # nope, convert to objects $memlist = [$self->get_members()]; } # add new member(s) push(@$memlist, @mems); # store if we created this array ref ourselves $self->sequences($memlist); # done return 1; } =head2 remove_members Title : remove_members Usage : Function: Remove the list of members for this cluster such that the member list is undefined afterwards (as opposed to zero members). Example : Returns : the previous list of members Args : none =cut sub remove_members{ my $self = shift; my @mems = $self->get_members(); $self->sequences(undef); return @mems; } =head2 next_locuslink Title : next_locuslink Usage : next_locuslink(); Function: Returns the next locuslink from an array referred to using $obj->{'locuslink'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $locuslink = $in->next_locuslink() ) { print "$locuslink\n"; } Returns : String Args : None =cut sub next_locuslink { my ($obj) = @_; return $obj->_next_element("ll","locuslink"); } =head2 next_express Title : next_express Usage : next_express(); Function: Returns the next tissue from an array referred to using $obj->{'express'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $express = $in->next_express() ) { print "$express\n"; } Returns : String Args : None =cut sub next_express { my ($obj) = @_; return $obj->_next_element("express","express"); } =head2 next_chromosome Title : next_chromosome Usage : next_chromosome(); Function: Returns the next chromosome line from an array referred to using $obj->{'chromosome'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $chromosome = $in->next_chromosome() ) { print "$chromosome\n"; } Returns : String Args : None =cut sub next_chromosome { my ($obj) = @_; return $obj->_next_element("chr","chromosome"); } =head2 next_protsim Title : next_protsim Usage : next_protsim(); Function: Returns the next protsim line from an array referred to using $obj->{'protsim'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $protsim = $in->next_protsim() ) { print "$protsim\n"; } Returns : String Args : None =cut sub next_protsim { my ($obj) = @_; return $obj->_next_element("protsim","protsim"); } =head2 next_sts Title : next_sts Usage : next_sts(); Function: Returns the next sts line from an array referred to using $obj->{'sts'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $sts = $in->next_sts() ) { print "$sts\n"; } Returns : String Args : None =cut sub next_sts { my ($obj) = @_; return $obj->_next_element("sts","sts"); } =head2 next_txmap Title : next_txmap Usage : next_txmap(); Function: Returns the next txmap line from an array referred to using $obj->{'txmap'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $tsmap = $in->next_txmap() ) { print "$txmap\n"; } Returns : String Args : None =cut sub next_txmap { my ($obj) = @_; return $obj->_next_element("txmap","txmap"); } ############################### # private method # # args: prefix name for the queue # name of the method from which to re-fill # returns: the next element from that queue, or undef if the queue is empty ############################### sub _next_element{ my ($self,$queuename,$meth) = @_; $queuename = "_".$queuename."_queue"; if(! exists($self->{$queuename})) { # re-initialize from array of sequence data $self->{$queuename} = [@{$self->$meth() }]; } my $queue = $self->{$queuename}; # is queue exhausted (equivalent to end of stream)? if(! @$queue) { # yes, remove queue and signal to the caller delete $self->{$queuename}; return; } return shift(@$queue); } =head1 L methods =cut =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences This is aliased to unigene_id(). Returns : A scalar =cut sub object_id { return shift->unigene_id(@_); } =head2 version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Unigene clusters usually won't have a version, so this will be mostly undefined. Returns : A number Args : on set, new value (a scalar or undef, optional) =cut sub version { my $self = shift; return $self->{'version'} = shift if @_; return $self->{'version'}; } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar Args : on set, new value (a scalar or undef, optional) =cut sub authority { my $self = shift; return $self->{'authority'} = shift if @_; return $self->{'authority'}; } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection Returns : A scalar Args : on set, new value (a scalar or undef, optional) =cut sub namespace { my $self = shift; return $self->{'namespace'} = shift if @_; return $self->{'namespace'}; } =head1 L methods =cut =head2 display_name Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) This is aliased to unigene_id(). Returns : A scalar Status : Virtual =cut sub display_name { return shift->unigene_id(@_); } =head2 description() Title : description Usage : $string = $obj->description() Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. The string should not be greater than 255 characters and clients can feel justified at truncating strings at 255 characters for the purposes of display This is already demanded by Bio::ClusterI and hence is present anyway. Returns : A scalar =cut =head1 L methods =cut =head2 next_seq Title : next_seq Usage : next_seq(); Function: Returns the next seq as a Seq object as defined by $seq->sequence_factory(), at present an empty Bio::Seq::RichSeq object with just the accession_number() and pid() set This iterator will not exhaust the array of member sequences. If you call next_seq() again after it returned undef, it will re-cycle through the list of member sequences. Example : while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } Returns : Bio::PrimarySeqI object Args : None =cut sub next_seq { my ($obj) = @_; if(! exists($obj->{'_seq_queue'})) { # re-initialize from array of sequence data $obj->{'_seq_queue'} = [@{$obj->sequences()}]; } my $queue = $obj->{'_seq_queue'}; # is queue exhausted (equivalent to end of stream)? if(! @$queue) { # yes, remove queue and signal to the caller delete $obj->{'_seq_queue'}; return; } # no, still data in the queue: get the next one from the queue my $seq_h = shift(@$queue); # if this is not a simple hash ref, it's an object already, and we'll # return just that return $seq_h if(ref($seq_h) ne 'HASH'); # nope, we need to assemble this object from scratch # # assemble the annotation collection my $ac = Bio::Annotation::Collection->new(); foreach my $k (keys %$seq_h) { next if $k =~ /acc|pid|nid|version/; my $ann = Bio::Annotation::SimpleValue->new(-tagname => $k, -value => $seq_h->{$k}); $ac->add_Annotation($ann); } # assemble the initialization parameters and create object my $seqobj = $obj->sequence_factory->create( -accession_number => $seq_h->{acc}, -pid => $seq_h->{pid}, # why does NCBI prepend a 'g' to its own identifiers?? -primary_id => $seq_h->{nid} && $seq_h->{nid} =~ /^g\d+$/ ? substr($seq_h->{nid},1) : $seq_h->{nid}, -display_id => $seq_h->{acc}, -seq_version => $seq_h->{version}, -alphabet => $obj->{'_alphabet'}, -namespace => $seq_h->{acc} =~ /^NM_/ ? 'RefSeq' : 'GenBank', -authority => $obj->authority(), # default is NCBI -species => $obj->species(), -annotation => $ac ); return $seqobj; } =head2 sequence_factory Title : sequence_factory Usage : $seqio->sequence_factory($seqfactory) Function: Get/Set the Bio::Factory::SequenceFactoryI Returns : Bio::Factory::SequenceFactoryI Args : [optional] Bio::Factory::SequenceFactoryI =cut sub sequence_factory { my ($self,$obj) = @_; if( defined $obj ) { if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) { $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)." sequence_factory()"); } $self->{'_seqfactory'} = $obj; } $self->{'_seqfactory'}; } =head1 Private methods =cut =head2 _annotation_value Title : _annotation_value Usage : Function: Private method. Example : Returns : the value (a string) Args : annotation key (a string) on set, annotation value (a string) =cut sub _annotation_value{ my $self = shift; my $key = shift; my ($ann, $val); if(@_) { $val = shift; if(! defined($val)) { ($ann) = $self->annotation->remove_Annotations($key); return $ann ? $ann->value() : undef; } } ($ann) = $self->annotation->get_Annotations($key); if(defined $ann && (! $val)) { # get mode and exists $val = $ann->value(); } elsif($val) { # set mode if(!defined $ann) { $ann = Bio::Annotation::SimpleValue->new(-tagname => $key); $self->annotation->add_Annotation($ann); } $ann->value($val); } return $val; } =head2 _annotation_value_ary Title : _annotation_value_ary Usage : Function: Private method. Example : Returns : reference to the array of values Args : annotation key (a string) on set, reference to an array holding the values =cut sub _annotation_value_ary{ my ($self,$key,$arr) = @_; my $ac = $self->annotation; if($arr) { # purge first $ac->remove_Annotations($key); # then add as many values as are present foreach my $val (@$arr) { my $ann = Bio::Annotation::SimpleValue->new(-value => $val, -tagname => $key ); $ac->add_Annotation($ann); } } else { my @vals = map { $_->value(); } $ac->get_Annotations($key); $arr = [@vals]; } return $arr; } =head2 _annotation_dblink Title : _annotation_dblink Usage : Function: Private method. Example : Returns : array of accessions for the given database (namespace) Args : annotation key (a string) dbname (a string) (optional on get, mandatory on set) on set, accession or ID (a string), and version =cut sub _annotation_dblink{ my ($self,$key,$dbname,$acc,$version) = @_; if($acc) { # set mode -- this is adding here my $ann = Bio::Annotation::DBLink->new(-tagname => $key, -primary_id => $acc, -database => $dbname, -version => $version); $self->annotation->add_Annotation($ann); return 1; } else { # get mode my @anns = $self->annotation->get_Annotations($key); # filter out those that don't match the requested database if($dbname) { @anns = grep { $_->database() eq $dbname; } @anns; } return map { $_->primary_id(); } @anns; } } =head2 _remove_dblink Title : _remove_dblink Usage : Function: Private method. Example : Returns : array of accessions for the given database (namespace) Args : annotation key (a string) dbname (a string) (optional) =cut sub _remove_dblink{ my ($self,$key,$dbname) = @_; my $ac = $self->annotation(); my @anns = (); if($dbname) { foreach my $ann ($ac->remove_Annotations($key)) { if($ann->database() eq $dbname) { push(@anns, $ann); } else { $ac->add_Annotation($ann); } } } else { @anns = $ac->remove_Annotations($key); } return map { $_->primary_id(); } @anns; } ##################################################################### # aliases for naming consistency or other reasons # ##################################################################### *sequence = \&sequences; 1; FamilyI.pm100644000765000024 1026013354321744 20617 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/Cluster# # BioPerl module for Bio::Cluster::FamilyI # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Cluster::FamilyI - Family Interface =head1 SYNOPSIS # see the implementations of this interface for details my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members = $cluster->get_members(-species=>"homo sapiens"); =head1 DESCRIPTION This interface if for a Family object representing a family of biological objects. A generic implementation for this may be found a L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Cluster::FamilyI; $Bio::Cluster::FamilyI::VERSION = '1.7.3'; use strict; use base qw(Bio::ClusterI); =head2 new We don't mandate but encourage implementors to support at least the following named parameters upon object initialization. Arguments Description --------- ----------- -family_id the name of the family -description the consensus description of the family -annotation_score the confidence by which the consensus description is representative of the family -members the members belonging to the family -alignment the multiple alignment of the members =cut =head2 family_id Title : family_id Usage : Bio::Cluster::FamilyI->family_id("znfp"); Function: get/set for the family id Returns : the family id Args : the family id =cut sub family_id{ shift->throw_not_implemented(); } =head2 family_score Title : family_score Usage : Bio::Cluster::FamilyI->family_score(95); Function: get/set for the score of algorithm used to generate the family if present Returns : the score Args : the score =cut sub family_score { shift->throw_not_implemented(); } =head1 Methods inherited from L =cut =head2 display_id Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args : =cut =head2 get_members Title : get_members Usage : Bio::Cluster::FamilyI->get_members(); Function: get the members of the family Returns : the array of members Args : the array of members =cut =head2 description Title : description Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein"); Function: get/set for the description of the family Returns : the description Args : the description =cut =head2 size Title : size Usage : Bio::Cluster::FamilyI->size(); Function: get/set for the description of the family Returns : size Args : =cut =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut 1; ClusterIO000755000765000024 013354321744 17000 5ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Biodbsnp.pm100644000765000024 2456013354321744 20633 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/ClusterIO# BioPerl module for Bio::ClusterIO::dbsnp # # Copyright Allen Day , Stan Nelson # Human Genetics, UCLA Medical School, University of California, Los Angeles # POD documentation - main docs before the code =head1 NAME Bio::ClusterIO::dbsnp - dbSNP input stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::ClusterIO class. =head1 DESCRIPTION Parse dbSNP XML files, one refSNP entry at a time. Note this handles dbSNPp output generated by NBCI's eutils and does NOT parse output derived from SNP's XML format (found at ftp://ftp.ncbi.nih.gov/snp/). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Allen Day Eallenday@ucla.eduE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::ClusterIO::dbsnp; $Bio::ClusterIO::dbsnp::VERSION = '1.7.3'; use strict; use Bio::Root::Root; use Bio::Variation::SNP; use XML::SAX; use Data::Dumper; use IO::File; use Time::HiRes qw(tv_interval gettimeofday); use base qw(Bio::ClusterIO); our $DEBUG = 0; our %MAPPING = ( #the ones commented out i haven't written methods for yet... -Allen 'Rs_rsId' => 'id', # 'Rs_taxId' => 'tax_id', # 'Rs_organism' => 'organism', 'Rs_snpType' => {'type' => 'value'}, 'Rs_sequence_observed' => 'observed', 'Rs_sequence_seq5' => 'seq_5', 'Rs_sequence_seq3' => 'seq_3', # 'Rs_sequence_exemplarSs' => 'exemplar_subsnp', 'Rs_create_build' => 'ncbi_build', #?? 'Rs_update_build' => 'ncbi_build', # 'NSE-rs_ncbi-num-chr-hits' => 'ncbi_chr_hits', # 'NSE-rs_ncbi-num-ctg-hits' => 'ncbi_ctg_hits', # 'NSE-rs_ncbi-num-seq-loc' => 'ncbi_seq_loc', # 'NSE-rs_ncbi-mapweight' => 'ncbi_mapweight', # 'NSE-rs_ucsc-build-id' => 'ucsc_build', # 'NSE-rs_ucsc-num-chr-hits' => 'ucsc_chr_hits', # 'NSE-rs_ucsc-num-seq-loc' => 'ucsc_ctg_hits', # 'NSE-rs_ucsc-mapweight' => 'ucsc_mapweight', 'Rs_het_value' => 'heterozygous', 'Rs_het-stdError' => 'heterozygous_SE', 'Rs_validation' => {'validated' => 'value'}, #?? # 'NSE-rs_genotype' => {'genotype' => 'value'}, 'Ss_handle' => 'handle', 'Ss_batchId' => 'batch_id', 'Ss_locSnpId' => 'id', # 'Ss_locSnpId' => 'loc_id', # 'Ss_orient' => {'orient' => 'value'}, # 'Ss_buildId' => 'build', 'Ss_methodClass' => {'method' => 'value'}, # 'NSE-ss_accession_E' => 'accession', # 'NSE-ss_comment_E' => 'comment', # 'NSE-ss_genename' => 'gene_name', # 'NSE-ss_assay-5_E' => 'seq_5', # 'NSE-ss_assay-3_E' => 'seq_3', # 'NSE-ss_observed' => 'observed', # 'NSE-ss-popinfo_type' => 'pop_type', # 'NSE-ss-popinfo_batch-id' => 'pop_batch_id', # 'NSE-ss-popinfo_pop-name' => 'pop_name', # 'NSE-ss-popinfo_samplesize' => 'pop_samplesize', # 'NSE-ss_popinfo_est-het' => 'pop_est_heterozygous', # 'NSE-ss_popinfo_est-het-se-sq' => 'pop_est_heterozygous_se_sq', # 'NSE-ss-alleleinfo_type' => 'allele_type', # 'NSE-ss-alleleinfo_batch-id' => 'allele_batch_id', # 'NSE-ss-alleleinfo_pop-id' => 'allele_pop_id', # 'NSE-ss-alleleinfo_snp-allele' => 'allele_snp', # 'NSE-ss-alleleinfo_other-allele' => 'allele_other', # 'NSE-ss-alleleinfo_freq' => 'allele_freq', # 'NSE-ss-alleleinfo_count' => 'allele_count', # 'NSE-rsContigHit_contig-id' => 'contig_hit', # 'NSE-rsContigHit_accession' => 'accession_hit', # 'NSE-rsContigHit_version' => 'version', # 'NSE-rsContigHit_chromosome' => 'chromosome_hit', # 'NSE-rsMaploc_asn-from' => 'asn_from', # 'NSE-rsMaploc_asn-to' => 'asn_to', # 'NSE-rsMaploc_loc-type' => {'loc_type' => 'value'}, # 'NSE-rsMaploc_hit-quality' => {'hit_quality' => 'value'}, # 'NSE-rsMaploc_orient' => {'orient' => 'value'}, # 'NSE-rsMaploc_physmap-str' => 'phys_from', # 'NSE-rsMaploc_physmap-int' => 'phys_to', 'FxnSet_geneId' => 'locus_id', # does the code realise that there can be multiple of these 'FxnSet_symbol' => 'symbol', 'FxnSet_mrnaAcc' => 'mrna', 'FxnSet_protAcc' => 'protein', 'FxnSet_fxnClass' => {'functional_class' => 'value'}, #... #... #there are lots more, but i don't need them at the moment... -Allen ); sub _initialize{ my ($self,@args) = @_; $self->SUPER::_initialize(@args); my ($usetempfile) = $self->_rearrange([qw(TEMPFILE)],@args); defined $usetempfile && $self->use_tempfile($usetempfile); # start up the parser factory my $parserfactory = XML::SAX::ParserFactory->parser( Handler => $self); $self->{'_xmlparser'} = $parserfactory; $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0); } =head2 next_cluster Title : next_cluster Usage : $dbsnp = $stream->next_cluster() Function: returns the next refSNP in the stream Returns : Bio::Variation::SNP object representing composite refSNP and its component subSNP(s). Args : NONE =cut ### #Adapted from Jason's blastxml.pm ### # you shouldn't have to preparse this; the XML is well-formed and refers # accurately to a remote DTD/schema sub next_cluster { my $self = shift; my $data = ''; my($tfh); if( $self->use_tempfile ) { $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!"); $tfh->autoflush(1); } my $start = 1; while( defined( $_ = $self->_readline ) ){ #skip to beginning of refSNP entry if($_ !~ m{]*>} && $start){ next; } elsif($_ =~ m{]*>} && $start){ $start = 0; } #slurp up the data if( defined $tfh ) { print $tfh $_; } else { $data .= $_; } #and stop at the end of the refSNP entry last if $_ =~ m{}; } #if we didn't find a start tag return if $start; my %parser_args; if( defined $tfh ) { seek($tfh,0,0); %parser_args = ('Source' => { 'ByteStream' => $tfh }, 'Handler' => $self); } else { %parser_args = ('Source' => { 'String' => $data }, 'Handler' => $self); } my $starttime; my $result; if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; } eval { $result = $self->{'_xmlparser'}->parse(%parser_args); }; if( $@ ) { $self->warn("error in parsing a report:\n $@"); $result = undef; } if( $DEBUG ) { $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime))); } return $self->refsnp; } =head2 SAX methods =cut =head2 start_document Title : start_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document. Creates a Bio::Variation::SNP Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{refsnp} = Bio::Variation::SNP->new; } sub refsnp { return shift->{refsnp}; } =head2 end_document Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : none Args : none =cut sub end_document{ my ($self,@args) = @_; } =head2 start_element Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data =cut sub start_element{ my ($self,$data) = @_; my $nm = $data->{'Name'}; my $at = $data->{'Attributes'}->{'{}value'}; #$self->debug(Dumper($at)) if $nm = ; if($nm eq 'Ss'){ $self->refsnp->add_subsnp; return; } if(my $type = $MAPPING{$nm}){ if(ref $type eq 'HASH'){ #okay, this is nasty. what can you do? $self->{will_handle} = (keys %$type)[0]; $self->{last_data} = $at->{Value}; } else { $self->{will_handle} = $type; $self->{last_data} = undef; } } else { undef $self->{will_handle}; } } =head2 end_element Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : none Args : hash ref for data =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $at = $data->{'Attributes'}; my $method = $self->{will_handle}; if($method){ if($nm =~ /^Rs/ or $nm =~ /^NSE-SeqLoc/ or $nm =~ /^FxnSet/){ $self->refsnp->$method($self->{last_data}); } elsif ($nm =~ /^Ss/){ $self->refsnp->subsnp->$method($self->{last_data}); } } } =head2 characters Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data' =cut sub characters{ my ($self,$data) = @_; $self->{last_data} = $data->{Data} if $data->{Data} =~ /\S/; #whitespace is meaningless -ad } =head2 use_tempfile Title : use_tempfile Usage : $obj->use_tempfile($newval) Function: Get/Set boolean flag on whether or not use a tempfile Example : Returns : value of use_tempfile Args : newvalue (optional) =cut sub use_tempfile{ my ($self,$value) = @_; if( defined $value) { $self->{'_use_tempfile'} = $value; } return $self->{'_use_tempfile'}; } 1; LittleChrY.dbsnp.xml100644000765000024 4055413354321744 21066 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/t/data Homo sapiens 9606 12345 0 0 52 2000-09-19 17:02 120 2004-10-04 13:37 14616 GGGTGGGCACTAGTTGGCGGGGTGGAAGGCACCACATTGGTCGCCTGCATGTCGTGGATGCA GCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT C/T GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGTAGCCAGGGTACT AGTAGCCAACCCACGTGCCACTCCGCACCCACACAGAT 14616 CGAP-GAI 607 59089 52 http://lpgws.nci.nih.gov:82/perl/gettrace.pl?type=7&trace= GGGTGGGCACTAGTTGGCGGGGTGGAAGGCACCACATTGGTCGCCTGCATGTCGTGGATGCA GCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT C/T GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGTAGCCAGGGTACT AGTAGCCAACCCACGTGCCACTCCGCACCCACACAGAT 1539216 LEE 3129 750160 92 http://www.bioinformatics.ucla.edu/snp/snp/snp_report.php3?db_ver sion=db_april_00&allele_id= ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC A/G ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC 4398532 LEE 5288 ge750160 106 ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC A/G ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC 4426703 LEE 5293 e750160 106 ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC A/G ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC 16250752 CGAP-GAI 8532 1500705 120 http://lpgws.nci.nih.gov/perl/gettrace.pl?type=7&trace= GTCGTGGATGCAGCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT C/T GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGT 125 34_3 reference 960600311 NT_011520.9 Hs22_11677_34 22 18933985 42112197 29807292 ref_haplotype reference 5246027 5246027 0.913983 24180013 24180012 99 101 5246026 5246028 3 0 1 1 1 0 1 1 125 35_1 Celera 960600397 NT_086921.1 Hs22_86581_35 22 18936537 48069707 51477137 alt_assembly_2 Celera 3888702 3888702 0.919897 22825240 22825239 99 101 3888701 3888703 3 0 1 1415 CRYBB2 NM_000496 1 NP_000487 1 1 1 0 1 0 125 35_1 reference 960600396 NT_011520.10 Hs22_11677_35 22 18933985 42210286 51476066 ref_haplotype reference 5246027 5246027 0.919897 24180013 24180012 99 101 5246026 5246028 3 0 1 1416 CRYBB2P1 1 1 0 1 1 125 3171883 24363 24363 0.913983 99 101 24362 24364 3 0 1 125 9863690 52075 52075 0.913983 99 101 52074 52076 3 0 1 125 51511751 24180012 24180012 0.913983 99 101 24180011 24180013 3 0 1 1 12345 UniGeneI.pm100644000765000024 2222313354321744 20732 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/Cluster# # BioPerl module for Bio::Cluster::UniGeneI.pm # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://anatomy.otago.ac.nz/meg # # You may distribute this module under the same terms as perl itself # # _history # April 31, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::Cluster::UniGeneI - abstract interface of UniGene object =head1 SYNOPSIS # =head1 DESCRIPTION This is the general interface for a UniGene cluster representation in Bioperl. You cannot use this module directly, use an implementation instead. You can create UniGene cluster objects yourself by instantiating L. If you read UniGene clusters from a ClusterIO parser, you will get objects implementing this interface, most likely instances of said UniGene class. L inherits from L, so you can use it wherever a cluster object is expected. =head1 FEEDBACK # =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Andrew Macgregor Email andrew at cbbc.murdoch.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Cluster::UniGeneI; $Bio::Cluster::UniGeneI::VERSION = '1.7.3'; use strict; use base qw(Bio::ClusterI); =head2 unigene_id Title : unigene_id Usage : unigene_id(); Function: Returns the unigene_id associated with the object. Example : $id = $unigene->unigene_id or $unigene->unigene_id($id) Returns : A string Args : None or an id =cut sub unigene_id { my ($self) = @_; $self->throw_not_implemented; } =head2 title Title : title Usage : title(); Function: Returns the title associated with the object. Example : $title = $unigene->title or $unigene->title($title) Returns : A string Args : None or a title =cut sub title { my ($self) = @_; $self->throw_not_implemented; } =head2 gene Title : gene Usage : gene(); Function: Returns the gene associated with the object. Example : $gene = $unigene->gene or $unigene->gene($gene) Returns : A string Args : None or a gene =cut sub gene { my ($self) = @_; $self->throw_not_implemented; } =head2 cytoband Title : cytoband Usage : cytoband(); Function: Returns the cytoband associated with the object. Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband) Returns : A string Args : None or a cytoband =cut sub cytoband { my ($self) = @_; $self->throw_not_implemented; } =head2 mgi Title : mgi Usage : mgi(); Function: Returns the mgi associated with the object. Example : $mgi = $unigene->mgi or $unigene->mgi($mgi) Returns : A string Args : None or a mgi =cut sub mgi { my ($self) = @_; $self->throw_not_implemented; } =head2 locuslink Title : locuslink Usage : locuslink(); Function: Returns or stores a reference to an array containing locuslink data. This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub locuslink { my ($self) = @_; $self->throw_not_implemented; } =head2 homol Title : homol Usage : homol(); Function: Returns the homol entry associated with the object. Example : $homol = $unigene->homol or $unigene->homol($homol) Returns : A string Args : None or a homol entry =cut sub homol { my ($self) = @_; $self->throw_not_implemented; } =head2 restr_expr Title : restr_expr Usage : restr_expr(); Function: Returns the restr_expr entry associated with the object. Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr) Returns : A string Args : None or a restr_expr entry =cut sub restr_expr { my ($self) = @_; $self->throw_not_implemented; } =head2 gnm_terminus Title : gnm_terminus Usage : gnm_terminus(); Function: Returns the gnm_terminus associated with the object. Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus) Returns : A string Args : None or a gnm_terminus =cut sub gnm_terminus { my ($self) = @_; $self->throw_not_implemented; } =head2 scount Title : scount Usage : scount(); Function: Returns the scount associated with the object. Example : $scount = $unigene->scount or $unigene->scount($scount) Returns : A string Args : None or a scount =cut sub scount { my ($self) = @_; $self->throw_not_implemented; } =head2 express Title : express Usage : express(); Function: Returns or stores a reference to an array containing tissue expression data. This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub express { my ($self) = @_; $self->throw_not_implemented; } =head2 chromosome Title : chromosome Usage : chromosome(); Function: Returns or stores a reference to an array containing chromosome lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub chromosome { my ($self) = @_; $self->throw_not_implemented; } =head2 sts Title : sts Usage : sts(); Function: Returns or stores a reference to an array containing sts lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub sts { my ($self) = @_; $self->throw_not_implemented; } =head2 txmap Title : txmap Usage : txmap(); Function: Returns or stores a reference to an array containing txmap lines Returns : An array reference Args : None or an array reference =cut sub txmap { my ($self) = @_; $self->throw_not_implemented; } =head2 protsim Title : protsim Usage : protsim(); Function: Returns or stores a reference to an array containing protsim lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub protsim { my ($self) = @_; $self->throw_not_implemented; } =head2 sequence Title : sequence Usage : sequence(); Function: Returns or stores a reference to an array containing sequence data This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub sequence { my ($self) = @_; $self->throw_not_implemented; } =head2 species Title : species Usage : $obj->species($newval) Function: Get the species object for this Unigene cluster. Example : Returns : value of species (a L object) Args : =cut sub species{ shift->throw_not_implemented(); } =head1 Methods inherited from L =cut =head2 display_id Title : display_id Usage : Function: Get/set the display name or identifier for the cluster Returns : a string Args : optional, on set the display ID ( a string) =cut =head2 description Title : description Usage : Bio::ClusterI->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster Returns : the description string Args : Optional the description string =cut =head2 size Title : size Usage : Bio::ClusterI->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family Args : =cut =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut =head2 get_members Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria, for example : $cluster->get_members(-species => 'homo sapiens'); Will return all members if no criteria are provided. Returns : the array of members Args : =cut 1; unigene.pm100644000765000024 2000713354321744 21147 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/ClusterIO# BioPerl module for Bio::ClusterIO::unigene # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://meg.otago.ac.nz # # You may distribute this module under the same terms as perl itself # # _history # April 17, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::ClusterIO::unigene - UniGene input stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::ClusterIO class. =head1 DESCRIPTION This object reads from Unigene *.data files downloaded from ftp://ftp.ncbi.nih.gov/repository/UniGene/. It does not download and decompress the file, you have to do that yourself. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Andrew Macgregor Email: andrew at cbbc.murdoch.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::ClusterIO::unigene; $Bio::ClusterIO::unigene::VERSION = '1.7.3'; use strict; use Bio::Cluster::UniGene; use Bio::Cluster::ClusterFactory; use base qw(Bio::ClusterIO); my %line_is = ( ID => q/ID\s+(\w{2,3}\.\d+)/, TITLE => q/TITLE\s+(\S.*)/, GENE => q/GENE\s+(\S.*)/, CYTOBAND => q/CYTOBAND\s+(\S.*)/, MGI => q/MGI\s+(\S.*)/, LOCUSLINK => q/LOCUSLINK\s+(\S.*)/, HOMOL => q/HOMOL\s+(\S.*)/, EXPRESS => q/EXPRESS\s+(\S.*)/, RESTR_EXPR => q/RESTR_EXPR\s+(\S.*)/, GNM_TERMINUS => q/GNM_TERMINUS\s+(\S.*)/, CHROMOSOME => q/CHROMOSOME\s+(\S.*)/, STS => q/STS\s+(\S.*)/, TXMAP => q/TXMAP\s+(\S.*)/, PROTSIM => q/PROTSIM\s+(\S.*)/, SCOUNT => q/SCOUNT\s+(\S.*)/, SEQUENCE => q/SEQUENCE\s+(\S.*)/, ACC => q/ACC=(\w+)(\.\d+)?/, NID => q/NID=\s*(\S.*)/, PID => q/PID=\s*(\S.*)/, CLONE => q/CLONE=\s*(\S.*)/, END => q/END=\s*(\S.*)/, LID => q/LID=\s*(\S.*)/, MGC => q/MGC=\s*(\S.*)/, SEQTYPE => q/SEQTYPE=\s*(\S.*)/, TRACE => q/TRACE=\s*(\S.*)/, PERIPHERAL => q/PERIPHERAL=\s*(\S.*)/, DELIMITER => q{^//}, ); # we set the right factory here sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); if(! $self->cluster_factory()) { $self->cluster_factory(Bio::Cluster::ClusterFactory->new( -type => 'Bio::Cluster::UniGene')); } } =head2 next_cluster Title : next_cluster Usage : $unigene = $stream->next_cluster() Function: returns the next unigene in the stream Returns : Bio::Cluster::UniGene object Args : NONE =cut sub next_cluster { my( $self) = @_; local $/ = "\n//"; return unless my $entry = $self->_readline; # set up the variables we'll need my (%unigene,@express,@locuslink,@chromosome, @sts,@txmap,@protsim,@sequence); my $UGobj; # set up the regexes # add whitespace parsing and precompile regexes #foreach (values %line_is) { # $_ =~ s/\s+/\\s+/g; # print STDERR "Regex is $_\n"; # #$_ = qr/$_/x; #} #$line_is{'TITLE'} = qq/TITLE\\s+(\\S.+)/; # run each line in an entry against the regexes foreach my $line (split /\n/, $entry) { #print STDERR "Wanting to match $line\n"; if ($line =~ /$line_is{ID}/gcx) { $unigene{ID} = $1; } elsif ($line =~ /$line_is{TITLE}/gcx ) { #print STDERR "MATCHED with [$1]\n"; $unigene{TITLE} = $1; } elsif ($line =~ /$line_is{GENE}/gcx) { $unigene{GENE} = $1; } elsif ($line =~ /$line_is{CYTOBAND}/gcx) { $unigene{CYTOBAND} = $1; } elsif ($line =~ /$line_is{MGI}/gcx) { $unigene{MGI} = $1; } elsif ($line =~ /$line_is{LOCUSLINK}/gcx) { @locuslink = split /;/, $1; } elsif ($line =~ /$line_is{HOMOL}/gcx) { $unigene{HOMOL} = $1; } elsif ($line =~ /$line_is{EXPRESS}/gcx) { my $express = $1; # remove initial semicolon if present $express =~ s/^;//; @express = split /\s*;/, $express; } elsif ($line =~ /$line_is{RESTR_EXPR}/gcx) { $unigene{RESTR_EXPR} = $1; } elsif ($line =~ /$line_is{GNM_TERMINUS}/gcx) { $unigene{GNM_TERMINUS} = $1; } elsif ($line =~ /$line_is{CHROMOSOME}/gcx) { push @chromosome, $1; } elsif ($line =~ /$line_is{TXMAP}/gcx) { push @txmap, $1; } elsif ($line =~ /$line_is{STS}/gcx) { push @sts, $1; } elsif ($line =~ /$line_is{PROTSIM}/gcx) { push @protsim, $1; } elsif ($line =~ /$line_is{SCOUNT}/gcx) { $unigene{SCOUNT} = $1; } elsif ($line =~ /$line_is{SEQUENCE}/gcx) { # parse into each sequence line my $seq = {}; # add unigene id to each seq #$seq->{unigene_id} = $unigene{ID}; my @items = split(/;/, $1); foreach (@items) { if (/$line_is{ACC}/gcx) { $seq->{acc} = $1; # remove leading dot if version pattern matched $seq->{version} = substr($2,1) if defined $2; } elsif (/$line_is{NID}/gcx) { $seq->{nid} = $1; } elsif (/$line_is{PID}/gcx) { $seq->{pid} = $1; } elsif (/$line_is{CLONE}/gcx) { $seq->{clone} = $1; } elsif (/$line_is{END}/gcx) { $seq->{end} = $1; } elsif (/$line_is{LID}/gcx) { $seq->{lid} = $1; } elsif (/$line_is{MGC}/gcx) { $seq->{mgc} = $1; } elsif (/$line_is{SEQTYPE}/gcx) { $seq->{seqtype} = $1; } elsif (/$line_is{TRACE}/gcx) { $seq->{trace} = $1; } elsif (/$line_is{PERIPHERAL}/gcx) { $seq->{peripheral} = $1; } } push @sequence, $seq; } elsif ($line =~ /$line_is{DELIMITER}/gcx) { # at the end of the record, add data to the object $UGobj = $self->cluster_factory->create_object( -display_id => $unigene{ID}, -description => $unigene{TITLE}, -size => $unigene{SCOUNT}, -members => \@sequence); $UGobj->gene($unigene{GENE}) if defined ($unigene{GENE}); $UGobj->cytoband($unigene{CYTOBAND}) if defined($unigene{CYTOBAND}); $UGobj->mgi($unigene{MGI}) if defined ($unigene{MGI}); $UGobj->locuslink(\@locuslink); $UGobj->homol($unigene{HOMOL}) if defined ($unigene{HOMOL}); $UGobj->express(\@express); $UGobj->restr_expr($unigene{RESTR_EXPR}) if defined ($unigene{RESTR_EXPR}); $UGobj->gnm_terminus($unigene{GNM_TERMINUS}) if defined ($unigene{GNM_TERMINUS}); $UGobj->chromosome(\@chromosome); $UGobj->sts(\@sts); $UGobj->txmap(\@txmap); $UGobj->protsim(\@protsim); } } return $UGobj; } 1; SequenceFamily.pm100644000765000024 2522213354321744 22203 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/Cluster# # BioPerl module for Bio::Cluster::SequenceFamily # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Cluster::SequenceFamily - Sequence Family object =head1 SYNOPSIS use Bio::SeqIO; use Bio::Cluster::SequenceFamily; use File::Spec; my $file = File::Spec->catfile('t','data','swiss.dat'); my $seqio= Bio::SeqIO->new(-format => 'swiss', -file => $file); my @mem; while(my $seq = $seqio->next_seq){ push @mem, $seq; } #create the family my $family = Bio::Cluster::SequenceFamily->new( -family_id=>"Family_1", -description=>"Family Description Here", -annotation_score=>"100", -members=>\@mem); #access the family foreach my $mem ($family->get_members){ print $mem->display_id."\t".$mem->desc."\n"; } #select members if members have a Bio::Species Object my @mem = $family->get_members(-binomial=>"Homo sapiens"); @mem = $family->get_members(-ncbi_taxid => 9606); @mem = $family->get_members(-common_name=>"Human"); @mem = $family->get_members(-species=>"sapiens"); @mem = $family->get_members(-genus=>"Homo"); =head1 DESCRIPTION This is a simple Family object that may hold any group of object. For more specific families, one should derive from FamilyI. =head1 FEEDBACK Email bioperl-l@bioperl.org for support and feedback. =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Cluster::SequenceFamily; $Bio::Cluster::SequenceFamily::VERSION = '1.7.3'; use strict; use warnings; use base qw(Bio::Root::Root Bio::Cluster::FamilyI); =head2 new Title : new Usage : my $family = Bio::Cluster::SequenceFamily->new( -family_id=>"Family_1", -description=>"Family Description Here", -annotation_score=>"100", -members=>\@mem); Function: Constructor for SequenceFamily object Returns : Bio::Cluster::SequenceFamily object See L. =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($id,$description,$version,$annot_score, $family_score,$members) = $self->_rearrange([qw(FAMILY_ID DESCRIPTION VERSION ANNOTATION_SCORE FAMILY_SCORE MEMBERS)],@args); $self->{'_members'} = []; $id && $self->family_id($id); $description && $self->description($description); $version && $self->version($version); $annot_score && $self->annotation_score($annot_score); $family_score && $self->family_score($family_score); $members && $self->add_members($members); return $self; } =head2 version Title : version Usage : $family->version("1.0"); Function: get/set for version Returns : a string version of the family generated. =cut sub version{ my ($self,$value) = @_; if($value){ $self->{'_version'} =$value; } return $self->{'_version'}; } =head2 annotation_score Title : annotation_score Usage : $family->annotation_score(100); Function: get/set for annotation_score which represent the confidence in which the consensus description has been assigned to the family. Returns : Bio::SimpleAlign See L =cut sub annotation_score{ my ($self,$score) = @_; if($score){ $self->{'_annotation_score'} = $score; } return $self->{'_annotation_score'}; } =head2 alignment Title : alignment Usage : $family->alignment($align); Function: get/set for an alignment object representing the multiple alignment of the members of the family. Returns : Bio::SimpleAlign See L =cut sub alignment { my ($self,$align) = @_; if($align){ $self->{'_alignment'} = $align; } return $self->{'_alignment'}; } =head2 tree Title : tree Usage : $family->tree($tree); Function: get/set for an tree object representing the phylogenetic tree of the family. Returns : Bio::Tree See L =cut sub tree { my ($self,$tree) = @_; if($tree) { $self->{'_tree'} = $tree; } return $self->{'_tree'}; } =head1 L methods =cut =head2 family_score Title : family_score Usage : Bio::Cluster::FamilyI->family_score(95); Function: get/set for the score of algorithm used to generate the family if present This is aliased to cluster_score(). Returns : the score Args : the score =cut sub family_score { return shift->cluster_score(@_); } =head2 family_id Title : family_id Usage : $family->family_id("Family_1"); Function: get/set for family id This is aliased to display_id(). Returns : a string specifying identifier of the family =cut sub family_id{ return shift->display_id(@_); } =head1 L methods =cut =head2 display_id Title : display_id Usage : Function: Get/set the display name or identifier for the cluster Returns : a string Args : optional, on set the display ID ( a string) =cut sub display_id{ my ($self,$id) = @_; if($id){ $self->{'_cluster_id'} = $id; } return $self->{'_cluster_id'}; } =head2 description Title : description Usage : $fam->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster Returns : the description string Args : Optional the description string =cut sub description{ my ($self,$desc) = @_; if($desc){ $self->{'_description'} = $desc; } return $self->{'_description'}; } =head2 get_members Title : get_members Usage : Valid criteria: -common_name -binomial -ncbi_taxid -organelle -genus $family->get_members(-common_name =>"human"); $family->get_members(-species =>"homo sapiens"); $family->get_members(-ncbi_taxid => 9606); For now, multiple critieria are ORed. Will return all members if no criteria are provided. Function: get members using methods from L the phylogenetic tree of the family. Returns : an array of objects that are member of this family. =cut sub get_members { my $self = shift; return @{$self->{'_members'}} unless @_; ## since the logic behind the checks is OR, we keep the ids in an hash for ## performance (skip the test if it's already there) and to avoid repats my %match; my %filter = @_; foreach my $key (keys %filter) { (my $method = $key) =~ s/^-//; %match = (%match, map { $_ => $_ } grep { ! $match{$_} && $_->species && ($_->species->can($method) || $self->throw("$method is an invalid criteria")) && $_->species->$method() eq $filter{$key} } @{$self->{'_members'}}); } return map {$match{$_}} keys (%match); } =head2 size Title : size Usage : $fam->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family Args : =cut sub size { my ($self) = @_; return scalar(@{$self->{'_members'}}); } =head2 cluster_score Title : cluster_score Usage : $fam->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut sub cluster_score{ my ($self,$score) = @_; if($score){ $self->{'_cluster_score'} = $score; } return $self->{'_cluster_score'}; } =head1 Implementation specific methods These are mostly for adding/removing/changing. =cut =head2 add_members Title : add_members Usage : $fam->add_member([$seq1,$seq1]); Function: add members to a family Returns : Args : the member(s) to add, as an array or arrayref =cut sub add_members{ my ($self,@mems) = @_; if (@mems) { my $mem = shift(@mems); if(ref($mem) eq "ARRAY"){ push @{$self->{'_members'}},@{$mem}; } else { push @{$self->{'_members'}},$mem; } push @{$self->{'_members'}}, @mems; } return 1; } =head2 remove_members Title : remove_members Usage : $fam->remove_members(); Function: remove all members from a family Returns : the previous array of members Args : none =cut sub remove_members{ my ($self) = @_; my $mems = $self->{'_members'}; $self->{'_members'} = []; return @$mems; } ##################################################################### # aliases for naming consistency or other reasons # ##################################################################### *flush_members = \&remove_members; *add_member = \&add_members; =head2 members Title : members Usage : $members = $fam->members([$seq1,$seq1]); Function: Deprecated. Use add_members() or get_members() instead =cut sub members{ my $self = shift; if(@_) { # this is in set mode $self->warn("setting members() in ".ref($self)." is deprecated.\n". "Use add_members() instead."); return $self->add_members(@_); } else { # get mode $self->warn("members() in ".ref($self)." is deprecated.\n". "Use get_members() instead."); return $self->get_members(); } } 1; ClusterFactory.pm100644000765000024 1232013354321744 22235 0ustar00cjfieldsstaff000000000000Bio-Cluster-1.7.3/lib/Bio/Cluster# # BioPerl module for Bio::Cluster::ClusterFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory =head1 SYNOPSIS use Bio::Cluster::ClusterFactory; # if you don't provide a default type, the factory will try # some guesswork based on display_id and namespace my $factory = Bio::Cluster::ClusterFactory->new(-type => 'Bio::Cluster::UniGene'); my $clu = $factory->create_object(-description => 'NAT', -display_id => 'Hs.2'); =head1 DESCRIPTION This object will build L objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Cluster::ClusterFactory; $Bio::Cluster::ClusterFactory::VERSION = '1.7.3'; use strict; use Bio::Root::Root; use base qw(Bio::Factory::ObjectFactory); =head2 new Title : new Usage : my $obj = Bio::Cluster::ClusterFactory->new(); Function: Builds a new Bio::Cluster::ClusterFactory object Returns : Bio::Cluster::ClusterFactory Args : -type => string, name of a ClusterI derived class. If not provided, the factory will have to guess from ID and namespace, which may or may not be successful. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->interface("Bio::ClusterI"); $self->type($self->type) if $self->type; return $self; } =head2 create_object Title : create_object Usage : my $seq = $factory->create_object(); Function: Instantiates new Bio::ClusterI (or one of its child classes) This object allows us to genericize the instantiation of cluster objects. Returns : L compliant object The return type is configurable using new(-type =>"..."). Args : initialization parameters specific to the type of cluster object we want. Typically -display_id => $name -description => description of the cluster -members => arrayref, members of the cluster =cut sub create_object { my ($self,@args) = @_; my $type = $self->type(); if(! $type) { # we need to guess this $type = $self->_guess_type(@args); $self->throw("No cluster type set and unable to guess.") unless $type; $self->type($type); } return $type->new(-verbose => $self->verbose, @args); } =head2 _guess_type Title : _guess_type Usage : Function: Guesses the right type of L implementation based on initialization parameters for the prospective object. Example : Returns : the type (a string, the module name) Args : initialization parameters to be passed to the prospective cluster object =cut sub _guess_type{ my ($self,@args) = @_; my $type; # we can only guess from a certain number of arguments my ($dispid, $ns, $members) = $self->_rearrange([qw(DISPLAY_ID NAMESPACE MEMBERS )], @args); # Unigene namespace or ID? if($ns && (lc($ns) eq "unigene")) { $type = 'Bio::Cluster::UniGene'; } elsif($dispid && ($dispid =~ /^Hs\.[0-9]/)) { $type = 'Bio::Cluster::UniGene'; } # what else could we look for? return $type; } 1;