Bio::FastParsers - Classes for parsing bioinformatic programs output
version 0.221230
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
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.
Denis BAURAIN <denis.baurain@uliege.be>
Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
Arnaud DI FRANCO <arnaud.difranco@gmail.com>
Aymeric NAOME <aymeric.naome@gmail.com>
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.
To install Bio::FastParsers, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::FastParsers
CPAN shell
perl -MCPAN -e shell install Bio::FastParsers
For more information on module installation, please visit the detailed CPAN module installation guide.