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package Bio::FastParsers; |
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# ABSTRACT: Classes for parsing bioinformatic programs output |
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# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be> |
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# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com> |
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$Bio::FastParsers::VERSION = '0.201110'; |
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use strict; |
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use warnings; |
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use Bio::FastParsers::Blast; |
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use Bio::FastParsers::Hmmer; |
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use Bio::FastParsers::CdHit; |
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use Bio::FastParsers::Uclust; |
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1; |
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__END__ |
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=pod |
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=head1 NAME |
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Bio::FastParsers - Classes for parsing bioinformatic programs output |
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=head1 VERSION |
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version 0.201110 |
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=head1 DESCRIPTION |
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This distribution includes modules for parsing the output files of a selection |
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of sequence comparison programs, including BLAST |
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L<https://blast.ncbi.nlm.nih.gov/>, HMMER L<http://hmmer.org/>, CD-HIT |
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L<https://github.com/weizhongli/cdhit> and UCLUST |
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L<http://www.drive5.com/usearch/>. |
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These classes are designed to add as few overhead as possible, using |
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constructs not far from those that would be found in home-made parsing |
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scripts. Moreover, their API stick closer to the behavior of each individual |
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software. In this respect, the approach of these parsers is very different |
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from Bioperl's L<Bio::SearchIO>. Hence, C<Bio::FastParsers> classes do not |
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need (and are not meant as a replacement for) L<BioPerl>. |
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C<Bio::FastParsers> modules have been used in production since 2013 but were |
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not yet ready for wider adoption due to their lack of documentation. This is |
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now nearly fixed: all modules are documented except for HMMER parsers. |
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=head1 AUTHOR |
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Denis BAURAIN <denis.baurain@uliege.be> |
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=head1 CONTRIBUTORS |
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=for stopwords Amandine BERTRAND Arnaud DI FRANCO |
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=over 4 |
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=item * |
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Amandine BERTRAND <amandine.bertrand@doct.uliege.be> |
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=item * |
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Arnaud DI FRANCO <arnaud.difranco@gmail.com> |
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=back |
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=head1 COPYRIGHT AND LICENSE |
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This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN. |
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This is free software; you can redistribute it and/or modify it under |
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the same terms as the Perl 5 programming language system itself. |
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=cut |