Bio::FastParsers(3)

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.