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Bio-FastParsers-0.180330
River stage one • 7 direct dependents • 8 total dependents
/ Bio::FastParsers

NAME

Bio::FastParsers - Classes for parsing bioinformatics programs output

VERSION

version 0.180330

DESCRIPTION

This distribution includes modules for parsing the output files of a selection of sequence comparison programs, such as BLAST https://blast.ncbi.nlm.nih.gov/ or HMMER http://hmmer.org/.

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 are not yet ready for wider adoption due to their lack of documentation. This should improve over time. Meanwhile, adventurous users can have a look at the Bio::FastParsers::Blast::Xml class which is already fully documented.

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTORS

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

  • Arnaud DI FRANCO <arnaud.difranco@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.