Bio::FastParsers - Classes for parsing bioinformatic programs output


version 0.201110


This distribution includes modules for parsing the output files of a selection of sequence comparison programs, including BLAST, HMMER, CD-HIT and UCLUST

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.


Denis BAURAIN <>


  • Amandine BERTRAND <>

  • Arnaud DI FRANCO <>


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.