package Bio::Gonzales;

use warnings;
use strict;

=head1 NAME

Bio::Gonzales - Speedy functions to manipulate biological data

=cut

our $VERSION = '0.078'; # VERSION


=head1 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, L<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 L<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');

=head1 DESCRIPTION

=head2 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 

=over 4

=item Working with genomic features (representation, grouping, GFF3 input/output)

=item Workgin with sequences (FASTA input/output, basic sequence manipulation and cleaning)

=item Multiple sequence alignment input/output

=item File and folder templates to organise computational experiments

=item BLAST & HMMER3 parsing

=item Standard utility functions




=back

=head2 Stable modules 

=head3 L<Bio::Gonzales::Seq::IO>

=head3 L<Bio::Gonzales::Range::Overlap>

=head3 L<Bio::Gonzales::Matrix::IO>

=head3 L<Bio::Gonzales::Seq>

=head3 L<Bio::Gonzales::Feat::IO::GFF3>

=head3 L<Bio::Gonzales::Feat>

=head3 L<Bio::Gonzales::Project::Functions>

=head2 Stable, but undocumented

=head3 L<Bio::Gonzales::Project>

=head3 L<Bio::Gonzales::MiniFeat>

=head1 AUTHOR

Joachim Bargsten, C<< <jwb at cpan.org> >>

=head1 BUGS

Please report any bugs or feature requests to C<bug-bargsten-bio at rt.cpan.org>, or through
the web interface at L<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.


=head1 SUPPORT

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

    perldoc Bio::Gonzales


You can also look for information at:

=over 4

=item * RT: CPAN's request tracker

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

=item * AnnoCPAN: Annotated CPAN documentation

L<http://annocpan.org/dist/Bio-Gonzales>

=item * CPAN Ratings

L<http://cpanratings.perl.org/d/Bio-Gonzales>

=item * Search CPAN

L<http://search.cpan.org/dist/Bio-Gonzales/>

=back


=head1 ACKNOWLEDGEMENTS


=head1 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.


=cut

1; # End of Bio::Gonzales