• NAME
• SYNOPSIS
• DESCRIPTION
  • Introdution
  • Stable modules
    • Bio::Gonzales::Seq::IO
    • Bio::Gonzales::Range::Overlap
    • Bio::Gonzales::Matrix::IO
    • Bio::Gonzales::Seq
    • Bio::Gonzales::Feat::IO::GFF3
    • Bio::Gonzales::Feat
    • Bio::Gonzales::Project::Functions
  • Stable, but undocumented
    • Bio::Gonzales::Project
    • Bio::Gonzales::MiniFeat
• AUTHOR
• BUGS
• SUPPORT
• ACKNOWLEDGEMENTS
• LICENSE AND COPYRIGHT

NAME

Bio::Gonzales - Speedy functions to manipulate biological data

SYNOPSIS

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');

DESCRIPTION

Introdution

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

Stable modules

Bio::Gonzales::Seq::IO

Bio::Gonzales::Range::Overlap

Bio::Gonzales::Matrix::IO

Bio::Gonzales::Seq

Bio::Gonzales::Feat::IO::GFF3

Bio::Gonzales::Feat

Bio::Gonzales::Project::Functions

Stable, but undocumented

Bio::Gonzales::Project

Bio::Gonzales::MiniFeat

AUTHOR

Joachim Bargsten, <jwb at cpan.org>

BUGS

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.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Bio::Gonzales

You can also look for information at:

• RT: CPAN's request tracker

  http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Gonzales

• AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/Bio-Gonzales

• CPAN Ratings

  http://cpanratings.perl.org/d/Bio-Gonzales

• Search CPAN

  http://search.cpan.org/dist/Bio-Gonzales/

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

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.