Bio-DB-Ace-1.7.3000755000765000024 013352276355 13266 5ustar00cjfieldsstaff000000000000Changes100644000765000024 33013352276355 14616 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3Summary of important user-visible changes for Bio-DB-Ace -------------------------------------------------------- 1.7.3 2018-09-24 19:10:19-05:00 America/Chicago * First release after split from bioperl-live. LICENSE100644000765000024 4410613352276355 14401 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3This software is copyright (c) 2018 by Ewan Birney , Lincoln Stein . 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 Ewan Birney , Lincoln Stein . 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. Mere aggregation of another independent work with the Program (or its derivative) on a volume of a storage or distribution medium does not bring the other work under the scope of these terms. 3. You may copy and distribute the Program (or a portion or derivative of it, under Paragraph 2) in object code or executable form under the terms of Paragraphs 1 and 2 above provided that you also do one of the following: a) accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Paragraphs 1 and 2 above; or, b) accompany it with a written offer, valid for at least three years, to give any third party free (except for a nominal charge for the cost of distribution) a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Paragraphs 1 and 2 above; or, c) accompany it with the information you received as to where the corresponding source code may be obtained. (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 Ewan Birney , Lincoln Stein . 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. You may otherwise modify your copy of this Package in any way, provided that you insert a prominent notice in each changed file stating how and when you changed that file, and provided that you do at least ONE of the following: a) place your modifications in the Public Domain or otherwise make them Freely Available, such as by posting said modifications to Usenet or an equivalent medium, or placing the modifications on a major archive site such as ftp.uu.net, or by allowing the Copyright Holder to include your modifications in the Standard Version of the Package. b) use the modified Package only within your corporation or organization. c) rename any non-standard executables so the names do not conflict with standard executables, which must also be provided, and provide a separate manual page for each non-standard executable that clearly documents how it differs from the Standard Version. d) make other distribution arrangements with the Copyright Holder. 4. You may distribute the programs of this Package in object code or executable form, provided that you do at least ONE of the following: a) distribute a Standard Version of the executables and library files, together with instructions (in the manual page or equivalent) on where to get the Standard Version. b) accompany the distribution with the machine-readable source of the Package with your modifications. c) accompany any non-standard executables with their corresponding Standard Version executables, giving the non-standard executables non-standard names, and clearly documenting the differences in manual pages (or equivalent), together with instructions on where to get the Standard Version. d) make other distribution arrangements with the Copyright Holder. 5. You may charge a reasonable copying fee for any distribution of this Package. You may charge any fee you choose for support of this Package. You may not charge a fee for this Package itself. 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 57013352276355 14775 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3name = Bio-DB-Ace version = 1.7.3 author = Ewan Birney , Lincoln Stein copyright_holder = Ewan Birney , Lincoln Stein 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 1575013352276355 14650 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3--- abstract: 'Database object interface to ACeDB servers' author: - 'Ewan Birney , Lincoln Stein ' build_requires: File::Spec: '0' IO::Handle: '0' IPC::Open3: '0' Test::More: '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-DB-Ace requires: Ace: '0' Ace::Sequence::Homol: '0' Bio::DB::Fasta: '0' Bio::DB::GFF::Adaptor::dbi::mysql: '0' Bio::DB::GFF::Adaptor::dbi::oracle: '0' Bio::DB::GFF::Util::Rearrange: '0' Bio::DB::RandomAccessI: '0' Bio::Seq: '0' base: '0' constant: '0' strict: '0' warnings: '0' resources: bugtracker: https://github.com/bioperl/bio-db-ace/issues homepage: https://metacpan.org/release/Bio-DB-Ace repository: git://github.com/bioperl/bio-db-ace.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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"class" : "Dist::Zilla::Plugin::FinderCode", "name" : ":MainModule", "version" : "6.010" }, { "class" : "Dist::Zilla::Plugin::FinderCode", "name" : ":AllFiles", "version" : "6.010" }, { "class" : "Dist::Zilla::Plugin::FinderCode", "name" : ":NoFiles", "version" : "6.010" } ], "zilla" : { "class" : "Dist::Zilla::Dist::Builder", "config" : { "is_trial" : 0 }, "version" : "6.010" } }, "x_serialization_backend" : "Cpanel::JSON::XS version 3.0239" } Makefile.PL100644000765000024 353413352276355 15326 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-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" => "Database object interface to ACeDB servers", "AUTHOR" => "Ewan Birney , Lincoln Stein ", "CONFIGURE_REQUIRES" => { "ExtUtils::MakeMaker" => 0 }, "DISTNAME" => "Bio-DB-Ace", "EXE_FILES" => [ "bin/bp_process_wormbase.pl" ], "LICENSE" => "perl", "MIN_PERL_VERSION" => "5.006", "NAME" => "Bio::DB::Ace", "PREREQ_PM" => { "Ace" => 0, "Ace::Sequence::Homol" => 0, "Bio::DB::Fasta" => 0, "Bio::DB::GFF::Adaptor::dbi::mysql" => 0, "Bio::DB::GFF::Adaptor::dbi::oracle" => 0, "Bio::DB::GFF::Util::Rearrange" => 0, "Bio::DB::RandomAccessI" => 0, "Bio::Seq" => 0, "base" => 0, "constant" => 0, "strict" => 0, "warnings" => 0 }, "TEST_REQUIRES" => { "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0 }, "VERSION" => "1.7.3", "test" => { "TESTS" => "t/*.t" } ); my %FallbackPrereqs = ( "Ace" => 0, "Ace::Sequence::Homol" => 0, "Bio::DB::Fasta" => 0, "Bio::DB::GFF::Adaptor::dbi::mysql" => 0, "Bio::DB::GFF::Adaptor::dbi::oracle" => 0, "Bio::DB::GFF::Util::Rearrange" => 0, "Bio::DB::RandomAccessI" => 0, "Bio::Seq" => 0, "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "base" => 0, "constant" => 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 $WriteMakefileArgs{CONFIGURE_REQUIRES} unless eval { ExtUtils::MakeMaker->VERSION(6.52) }; WriteMakefile(%WriteMakefileArgs); t000755000765000024 013352276355 13452 5ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.300-compile.t100644000765000024 530213352276355 15644 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/tuse 5.006; use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::Compile 2.057 use Test::More; plan tests => 5 + ($ENV{AUTHOR_TESTING} ? 1 : 0); my @module_files = ( 'Bio/DB/Ace.pm', 'Bio/DB/GFF/Adaptor/ace.pm', 'Bio/DB/GFF/Adaptor/dbi/mysqlace.pm', 'Bio/DB/GFF/Adaptor/dbi/oracleace.pm' ); my @scripts = ( 'bin/bp_process_wormbase.pl' ); # 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; } } foreach my $file (@scripts) { SKIP: { open my $fh, '<', $file or warn("Unable to open $file: $!"), next; my $line = <$fh>; close $fh and skip("$file isn't perl", 1) unless $line =~ /^#!\s*(?:\S*perl\S*)((?:\s+-\w*)*)(?:\s*#.*)?$/; @switches = (@switches, split(' ', $1)) if $1; my $stderr = IO::Handle->new; diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } $^X, @switches, '-c', $file)) if $ENV{PERL_COMPILE_TEST_DEBUG}; my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-c', $file); binmode $stderr, ':crlf' if $^O eq 'MSWin32'; my @_warnings = <$stderr>; waitpid($pid, 0); is($?, 0, "$file compiled ok"); shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ and not eval { +require blib; blib->VERSION('1.01') }; # in older perls, -c output is simply the file portion of the path being tested if (@_warnings = grep { !/\bsyntax OK$/ } grep { chomp; $_ ne (File::Spec->splitpath($file))[2] } @_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}; DB000755000765000024 013352276355 14753 5ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/BioAce.pm100644000765000024 1133613352276355 16165 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/Bio/DB # # BioPerl module for Bio::DB::Ace # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Ace - Database object interface to ACeDB servers =head1 SYNOPSIS $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000'); $seq = $db->get_Seq_by_id('J00522'); # Unique ID # or ... $seq = $db->get_Seq_by_acc('J00522'); # Accession Number =head1 DESCRIPTION This provides a standard BioPerl database access to Ace, using Lincoln Steins excellent AcePerl module. You need to download and install the aceperl module from http://stein.cshl.org/AcePerl/ before this interface will work. This interface is designed at the moment to work through a aceclient/aceserver type mechanism =head1 INSTALLING ACEPERL Download the latest aceperl tar file, gunzip/untar and cd into the directory. This is a standard CPAN-style directory, so if you go Perl Makefile.PL make make install Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere. =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 - Ewan Birney Email birney@ebi.ac.uk =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::DB::Ace; $Bio::DB::Ace::VERSION = '1.7.3'; use strict; # Object preamble - inherits from Bio::DB::RandomAccessI use Bio::Seq; BEGIN { eval "require Ace;"; if( $@) { print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@"; } } use base qw(Bio::DB::RandomAccessI); # new() is inherited from Bio::DB::Abstract # _initialize is where the heavy stuff will happen when new is called sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($host,$port) = $self->_rearrange([qw( HOST PORT )], @args, ); if( !$host || !$port ) { $self->throw("Must have a host and port for an acedb server to work"); } my $aceobj = Ace->connect(-host => $host, -port => $port) || $self->throw("Could not make acedb object to $host:$port"); $self->_aceobj($aceobj); return $self; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id($uid); Function: Gets a Bio::Seq object by its unique identifier/name Returns : a Bio::Seq object Args : $id : the id (as a string) of the desired sequence entry =cut sub get_Seq_by_id { my $self = shift; my $id = shift or $self->throw("Must supply an identifier!\n"); my $ace = $self->_aceobj(); my ($seq,$dna,$out); $seq = $ace->fetch( 'Sequence' , $id); # get out the sequence somehow! $dna = $seq->asDNA(); $dna =~ s/^>.*\n//; $dna =~ s/\n//g; $out = Bio::Seq->new( -id => $id, -alphabet => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id"); return $out; } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a Bio::Seq object by its accession number Returns : a Bio::Seq object Args : $acc : the accession number of the desired sequence entry =cut sub get_Seq_by_acc { my $self = shift; my $acc = shift or $self->throw("Must supply an accession number!\n"); return $self->get_Seq_by_id($acc); } =head2 _aceobj Title : _aceobj Usage : $ace = $db->_aceobj(); Function: Get/Set on the acedb object Returns : Ace object Args : New value of the ace object =cut sub _aceobj { my ($self,$arg) = @_; if( $arg ) { $self->{'_aceobj'} = $arg; } return $self->{'_aceobj'}; } 1; author-mojibake.t100644000765000024 35313352276355 17041 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/t#!perl BEGIN { unless ($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(); author-pod-syntax.t100644000765000024 45413352276355 17370 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests. use strict; use warnings; use Test::More; use Test::Pod 1.41; all_pod_files_ok(); bin000755000765000024 013352276355 13757 5ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3bp_process_wormbase.pl100644000765000024 1676513352276355 20551 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/bin#!/usr/bin/perl use constant ACEDB => 'sace://aceserver.cshl.org:2005'; use strict; use warnings; use Ace; my @framework = qw(mex-3 spe-15 lin-17 unc-11 dhc-1 unc-40 smg-5 unc-13 unc-29 eat-16 lin-11 spe-9 par-6 unc-59 unc-54 mab-9 lin-42 sri-71 smu-2 vab-1 bli-2 dpy-10 him-14 mig-5 unc-4 bli-1 sqt-1 rol-1 his-14 unc-52 unc-45 par-2 let-805 sel-8 mab-21 daf-4 sma-3 lin-39 unc-32 tax-4 ced-9 tra-1 nob-1 daf-1 ced-2 lin-1 unc-17 dpy-13 unc-5 smg-7 dif-1 lin-49 elt-1 daf-14 dpy-20 dpy-26 unc-30 tra-3 sup-24 rho-1 egl-8 unc-60 srh-36 apx-1 unc-62 let-418 dpy-11 let-413 sel-9 unc-42 egl-9 sma-1 sqt-3 odr-3 hda-1 unc-76 gcy-20 skr-5 par-4 unc-51 egl-17 lim-6 fox-1 fax-1 lon-2 unc-97 unc-6 unc-18 mec-10 sop-1 mab-18 sdc-2 odr-7 unc-9 unc-3 gas-1 ace-1); my %framework = map {$_=>1} @framework; my %framework_seen = (); my $USAGE = < wormbase.gff It may take a while before you see output from this script, since it must first fetch gene and protein database from the remote AceDB running at www.wormbase.org. The wormbase.gff file can then be loaded into a Bio::DB::GFF database using the following command: % bulk_load_gff.pl -d wormbase.gff USAGE ; #' die $USAGE if $ARGV[0]=~/^-?-h/i; my $db = Ace->connect(-url=>ACEDB, -query_timeout=>500) or die "Can't open ace database:",Ace->error; if (-d $ARGV[0]) { @ARGV = <$ARGV[0]/*.gff.gz>; } @ARGV || die $USAGE; foreach (@ARGV) { # GFF FILES $_ = "gunzip -c $_ |" if /\.gz$/; } my (%NOTES,%LOCUS,%GENBANK,%CONFIRMED,%ORFEOME); get_confirmed($db,\%CONFIRMED); get_genbank($db,\%GENBANK); get_loci($db,\%LOCUS); get_notes($db,\%NOTES); get_orfeome($db,\%ORFEOME); while (<>) { chomp; next if /^\#/; my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split /\t/; next if $source eq 'assembly_tag'; # don't want 'em, don't need 'em $ref =~ s/^CHROMOSOME_//; $group =~ s/CHROMOSOME_//; $source ='' if $source eq '*UNKNOWN*'; if ($method eq 'Sequence' && ($source eq 'curated' || $source eq 'RNA') && $group =~ /Sequence "(\w+\.\d+[a-z]?)"/) { my @notes; push @notes,map { qq(Note "$_") } @{$NOTES{$1}} if $NOTES{$1}; push @notes,map { qq(Note "$_") } @{$LOCUS{$1}} if $LOCUS{$1}; push @notes,qq(Confirmed_by "$CONFIRMED{$1}") if $CONFIRMED{$1}; $group = join ' ; ',$group,@notes; if (my $loci = $LOCUS{$1}) { foreach (@$loci) { print join("\t",$ref,$source,'gene',$start,$stop,$score,$strand,$phase,"Locus $_"),"\n"; print join("\t",$ref,'framework','gene',$start,$stop,$score,$strand,$phase,"Locus $_"),"\n" if $framework{$_} && !$framework_seen{$_}++; } } } if ($method eq 'Sequence' && $source eq 'Genomic_canonical' && $group =~ /Sequence "(\w+)"/) { if (my $accession = $GENBANK{$1}) { $group .= qq( ; Note "Genbank $accession"); print join("\t",$ref,'Genbank',$method,$start,$stop,$score,$strand,$phase,"Genbank \"$accession\""),"\n"; } } if ($method eq 'reagent' && $source eq 'Orfeome_project' && $group =~ /PCR_product "([^\"]+)"/) { my $amp = $ORFEOME{$1}; $group .= qq( ; Amplified $amp) if defined $amp; } # fix variant fields: Variant "T" => Note "T" $group =~ s/(?:Variant|Insert) "(\w+)"/Note "$1"/; # fix UTR fields if ($group =~ /UTR "([35])_UTR:(\S+)"/) { $method = 'UTR'; $source = "$1_UTR"; $group = qq(Sequence "$2"); } print join("\t",$ref,$source,$method,$start,$stop,$score,$strand,$phase,$group),"\n"; } sub get_loci { my ($db,$hash) = @_; # hash keys are predicted gene names, values are one or more loci names my @genes = $db->fetch(-query=>'find Locus Genomic_sequence',-filltag=>'Genomic_sequence'); foreach my $obj (@genes) { my @genomic = $obj->Genomic_sequence or next; foreach (@genomic) { push @{$hash->{$_}},$obj; } } } sub get_notes { my ($db,$hash) = @_; # hash keys are predicted gene names, values are one or more brief identifications my @genes = $db->fetch(-query=>'find Sequence Brief_identification',-filltag=>'Brief_identification'); foreach my $obj (@genes) { my @notes = $obj->Brief_identification or next; $hash->{$obj} = \@notes; } } sub get_genbank { my ($db,$hash) = @_; # hash keys are cosmid names, values are genbank accessions (1 to 1) my @cosmids = $db->fetch(-query=>'find Genome_Sequence Database',-filltag=>'Database'); for my $cosmid (@cosmids) { my ($database,undef,$accession) = $cosmid->Database(1)->row; next unless $accession; $hash->{$cosmid} = $accession; } } sub get_confirmed { my ($db,$hash) = @_; # hash keys are predicted gene names, values are confirmation type my @confirmed = $db->fetch(-query=>'find Sequence Confirmed_by',-filltag=>'Confirmed_by'); foreach my $obj (@confirmed) { my $confirmed_by = $obj->Confirmed_by || 'Unknown'; $hash->{$obj} = $confirmed_by; } } sub get_orfeome { my ($db,$hash) = @_; my @mv_primers = $db->fetch(-query=>'find PCR_Product mv*',-filltag=>'Amplified'); for my $obj (@mv_primers) { my $amplified = $obj->Amplified; $hash->{$obj} = $amplified; } } __END__ =head1 NAME bp_process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser =head1 SYNOPSIS % bp_process_wormbase.pl ./WS61 > wormbase.gff =head1 DESCRIPTION This script massages the Wormbase GFF files located at ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the GFF format suitable for display by the generic genome browser. It mainly adds comments to the annotations and designates certain well-spaced genetic loci as framework landmarks. This script requires the AcePerl distribution, which is available on CPAN (look for the "Ace" module). To use this script, get the WormBase GFF files from the FTP site listed above and place them in a directory. It might be a good idea to name the directory after the current release, such as WS61. You do not need to uncompress the files. Then give that directory as the argument to this script and capture the script's output to a file: % bp_process_wormbase.pl ./WS61 > wormbase.gff It may take a while before you see output from this script, since it must first fetch gene and protein database from the remote AceDB running at www.wormbase.org. The wormbase.gff file can then be loaded into a Bio::DB::GFF database using the following command: % bulk_load_gff.pl -d wormbase.gff =head1 SEE ALSO L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE Copyright (c) 2002 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. =cut Adaptor000755000765000024 013352276355 16747 5ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/Bio/DB/GFFace.pm100644000765000024 250413352276355 20176 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/Bio/DB/GFF/Adaptorpackage Bio::DB::GFF::Adaptor::ace; $Bio::DB::GFF::Adaptor::ace::VERSION = '1.7.3'; =head1 NAME Bio::DB::GFF::Adaptor::ace -- ace interface (for multiple inheritance) =head1 SYNOPSIS Pending See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Ace; use Bio::DB::GFF::Util::Rearrange; # for rearrange() sub dna_db { my $self = shift; my $d = $self->{dna_db}; $self->{dna_db} = shift if @_; $d; } sub acedb { my $self = shift; my $d = $self->{acedb}; $self->{acedb} = shift if @_; $d; } =head2 freshen_ace Title : freshen Usage : $flag = Bio::DB::GFF->freshen_ace; Function: Refresh internal acedb handle Returns : flag if correctly freshened Args : none Status : Public ACeDB has an annoying way of timing out, leaving dangling database handles. This method will invoke the ACeDB reopen() method, which causes dangling handles to be refreshed. It has no effect if you are not using ACeDB to create ACeDB objects. =cut sub freshen_ace { my $acedb = shift->acedb or return; $acedb->reopen(); } 1; dbi000755000765000024 013352276355 17505 5ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/Bio/DB/GFF/Adaptormysqlace.pm100644000765000024 562113352276355 22025 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/Bio/DB/GFF/Adaptor/dbipackage Bio::DB::GFF::Adaptor::dbi::mysqlace; $Bio::DB::GFF::Adaptor::dbi::mysqlace::VERSION = '1.7.3'; =head1 NAME Bio::DB::GFF::Adaptor::dbi::mysqlace -- Unholy union between mysql GFF database and acedb database =head1 SYNOPSIS Pending See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use base qw(Bio::DB::GFF::Adaptor::dbi::mysql Bio::DB::GFF::Adaptor::ace); # Create a new Bio::DB::GFF::Adaptor::dbi object sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($dna_db,$acedb) = rearrange([[qw(DNADB DNA FASTA FASTA_DIR)],'ACEDB'],@_); if ($dna_db) { if (!ref($dna_db)) { require Bio::DB::Fasta; my $fasta_dir = $dna_db; $dna_db = Bio::DB::Fasta->new($fasta_dir); $dna_db or $class->throw("new(): Failed to create new Bio::DB::Fasta from files in $fasta_dir"); } else { $dna_db->isa('Bio::DB::Fasta') or $class->throw("new(): $dna_db is not a Bio::DB::Fasta object"); } $self->dna_db($dna_db); } if ($acedb) { $acedb->isa('Ace') or $class->throw("$acedb is not an acedb accessor object"); $self->acedb($acedb); } $self; } =head2 freshen_ace Title : freshen Usage : $flag = Bio::DB::GFF->freshen_ace; Function: Refresh internal acedb handle Returns : flag if correctly freshened Args : none Status : Public ACeDB has an annoying way of timing out, leaving dangling database handles. This method will invoke the ACeDB reopen() method, which causes dangling handles to be refreshed. It has no effect if you are not using ACeDB to create ACeDB objects. =cut ######################### # Moved from mysqlopt.pm ######################### sub make_object { my $self = shift; my ($class,$name,$start,$stop) = @_; if (my $db = $self->acedb) { # for Notes we just return a text, no database associated return $class->new(Text=>$name) if $class eq 'Note'; # for homols, we create the indicated Protein or Sequence object # then generate a bogus Homology object (for future compatability??) if ($start ne '') { require Ace::Sequence::Homol; return Ace::Sequence::Homol->new_homol($class,$name,$db,$start,$stop); } # General case: my $obj = $db->class->new($class=>$name,$self->acedb); return $obj if defined $obj; # Last resort, return a Text return $class->new(Text=>$name); } return $self->SUPER::make_object($class,$name,$start,$stop); } sub get_dna { my $self = shift; my ($ref,$start,$stop,$class) = @_; my $dna_db = $self->dna_db or return $self->SUPER::get_dna(@_); return $dna_db->seq($ref,$start,$stop,$class); } 1; oracleace.pm100644000765000024 551213352276355 22124 0ustar00cjfieldsstaff000000000000Bio-DB-Ace-1.7.3/lib/Bio/DB/GFF/Adaptor/dbipackage Bio::DB::GFF::Adaptor::dbi::oracleace; $Bio::DB::GFF::Adaptor::dbi::oracleace::VERSION = '1.7.3'; =head1 NAME Bio::DB::GFF::Adaptor::dbi::oracleace -- Unholy union between oracle GFF database and acedb database =head1 SYNOPSIS Pending See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use base qw(Bio::DB::GFF::Adaptor::ace Bio::DB::GFF::Adaptor::dbi::oracle); # Create a new Bio::DB::GFF::Adaptor::dbi object sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($dna_db,$acedb) = rearrange([[qw(DNADB DNA FASTA FASTA_DIR)],'ACEDB'],@_); if ($dna_db) { if (!ref($dna_db)) { require Bio::DB::Fasta; my $fasta_dir = $dna_db; $dna_db = Bio::DB::Fasta->new($fasta_dir); $dna_db or $class->throw("new(): Failed to create new Bio::DB::Fasta from files in $fasta_dir"); } else { $dna_db->isa('Bio::DB::Fasta') or $class->throw("new(): $dna_db is not a Bio::DB::Fasta object"); } $self->dna_db($dna_db); } if ($acedb) { $acedb->isa('Ace') or $class->throw("$acedb is not an acedb accessor object"); $self->acedb($acedb); } $self; } sub make_object { my $self = shift; my ($class,$name,$start,$stop) = @_; if (my $db = $self->acedb) { # for Notes we just return a text, no database associated return $class->new(Text=>$name) if $class eq 'Note'; # for homols, we create the indicated Protein or Sequence object # then generate a bogus Homology object (for future compatability??) if ($start ne '') { require Ace::Sequence::Homol; return Ace::Sequence::Homol->new_homol($class,$name,$db,$start,$stop); } # General case: my $obj = $db->class->new($class=>$name,$self->acedb); return $obj if defined $obj; # Last resort, return a Text return $class->new(Text=>$name); } return $self->SUPER::make_object($class,$name,$start,$stop); } sub get_dna { my $self = shift; my ($ref,$start,$stop,$class) = @_; my $dna_db = $self->dna_db or return $self->SUPER::get_dna(@_); return $dna_db->seq($ref,$start,$stop,$class); } =head2 freshen_ace Title : freshen Usage : $flag = Bio::DB::GFF->freshen_ace; Function: Refresh internal acedb handle Returns : flag if correctly freshened Args : none Status : Public ACeDB has an annoying way of timing out, leaving dangling database handles. This method will invoke the ACeDB reopen() method, which causes dangling handles to be refreshed. It has no effect if you are not using ACeDB to create ACeDB objects. =cut 1;