02 Jan 2021 23:10:48 UTC
- Distribution: Bio-Gonzales
- Module version: 0.083
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- License: perl_5
- Perl: v5.10.0
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Bio::Gonzales - Speedy functions to manipulate biological data
Biological data analysis is often cumbersome: most tasks are very similar, but still there is a small difference between them. Bio::Gonzales gives you the modules and functions that make data crunching easy and speedy, while keeping the flexibility.
It should not be complete, the focus relies on a few standard formats. If one is burning in format hell, Bio::Perl might be a much better complement.
To outline the simple usage, here an example to read a fasta sequence file into a array of Bio::Gonzales::Seq objects.
use Bio::Gonzales::Seq::IO qw/faslurp/; my @seqs = faslurp('sequences.fa'); # Oh, f**k, somebody sent me gzipped fasta files! # Calm down! Gonzales has a speedy answer for that: my @seqs = faslurp('sequences.fa.gz');
Motivation for this package is the lack of speed or ease of use or both in other modules. The main branches are grouped into
- Working with genomic features (representation, grouping, GFF3 input/output)
- Workgin with sequences (FASTA input/output, basic sequence manipulation and cleaning)
- Multiple sequence alignment input/output
- File and folder templates to organise computational experiments
- BLAST & HMMER3 parsing
- Standard utility functions
<jwb at cpan.org>
Please report any bugs or feature requests to
bug-bargsten-bio at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Gonzales. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
You can find documentation for this module with the perldoc command.
You can also look for information at:
RT: CPAN's request tracker
AnnoCPAN: Annotated CPAN documentation
Copyright 2010 Joachim Bargsten.
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.
See http://dev.perl.org/licenses/ for more information.
Module Install Instructions
To install Bio::Gonzales, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::Gonzales
For more information on module installation, please visit the detailed CPAN module installation guide.