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Bio-FastParsers-0.221230
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/ Bio::FastParsers

NAME

Bio::FastParsers - Classes for parsing bioinformatic programs output

VERSION

version 0.221230

DESCRIPTION

This distribution includes modules for parsing the output files of a selection of sequence comparison programs, including BLAST https://blast.ncbi.nlm.nih.gov/, HMMER http://hmmer.org/, CD-HIT https://github.com/weizhongli/cdhit and UCLUST http://www.drive5.com/usearch/.

These classes are designed to add as few overhead as possible, using constructs not far from those that would be found in home-made parsing scripts. Moreover, their API stick closer to the behavior of each individual software. In this respect, the approach of these parsers is very different from Bioperl's Bio::SearchIO. Hence, Bio::FastParsers classes do not need (and are not meant as a replacement for) BioPerl.

Bio::FastParsers modules have been used in production since 2013 but were not yet ready for wider adoption due to their lack of documentation. This is now nearly fixed: all modules are documented except for HMMER parsers.

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTORS

  • Amandine BERTRAND <amandine.bertrand@doct.uliege.be>

  • Arnaud DI FRANCO <arnaud.difranco@gmail.com>

  • Aymeric NAOME <aymeric.naome@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.