File Coverage

blib/lib/Bio/Gonzales.pm
Criterion Covered Total %
statement 6 6 100.0
branch n/a
condition n/a
subroutine 2 2 100.0
pod n/a
total 8 8 100.0


line stmt bran cond sub pod time code
1             package Bio::Gonzales;
2              
3 1     1   122734 use warnings;
  1         2  
  1         35  
4 1     1   8 use strict;
  1         2  
  1         63  
5              
6             =head1 NAME
7              
8             Bio::Gonzales - Speedy functions to manipulate biological data
9              
10             =cut
11              
12             our $VERSION = '0.083'; # VERSION
13              
14              
15             =head1 SYNOPSIS
16              
17             Biological data analysis is often cumbersome: most tasks are very similar, but
18             still there is a small difference between them. Bio::Gonzales gives you the
19             modules and functions that make data crunching easy and speedy, while keeping the
20             flexibility.
21              
22             It should not be complete, the focus relies on a few standard formats. If one
23             is burning in format hell, L<Bio::Perl> might be a much better complement.
24              
25             To outline the simple usage, here an example to read a fasta sequence file
26             into a array of L<Bio::Gonzales::Seq> objects.
27              
28              
29             use Bio::Gonzales::Seq::IO qw/faslurp/;
30              
31             my @seqs = faslurp('sequences.fa');
32              
33             # Oh, f**k, somebody sent me gzipped fasta files!
34             # Calm down! Gonzales has a speedy answer for that:
35              
36             my @seqs = faslurp('sequences.fa.gz');
37              
38             =head1 DESCRIPTION
39              
40             =head2 Introdution
41              
42             Motivation for this package is the lack of speed or ease of use or both in other modules.
43             The main branches are grouped into
44              
45             =over 4
46              
47             =item Working with genomic features (representation, grouping, GFF3 input/output)
48              
49             =item Workgin with sequences (FASTA input/output, basic sequence manipulation and cleaning)
50              
51             =item Multiple sequence alignment input/output
52              
53             =item File and folder templates to organise computational experiments
54              
55             =item BLAST & HMMER3 parsing
56              
57             =item Standard utility functions
58              
59              
60              
61              
62             =back
63              
64             =head2 Stable modules
65              
66             =head3 L<Bio::Gonzales::Seq::IO>
67              
68             =head3 L<Bio::Gonzales::Range::Overlap>
69              
70             =head3 L<Bio::Gonzales::Matrix::IO>
71              
72             =head3 L<Bio::Gonzales::Seq>
73              
74             =head3 L<Bio::Gonzales::Feat::IO::GFF3>
75              
76             =head3 L<Bio::Gonzales::Feat>
77              
78             =head3 L<Bio::Gonzales::Project::Functions>
79              
80             =head2 Stable, but undocumented
81              
82             =head3 L<Bio::Gonzales::Project>
83              
84             =head3 L<Bio::Gonzales::MiniFeat>
85              
86             =head1 AUTHOR
87              
88             Joachim Bargsten, C<< <jwb at cpan.org> >>
89              
90             =head1 BUGS
91              
92             Please report any bugs or feature requests to C<bug-bargsten-bio at rt.cpan.org>, or through
93             the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Gonzales>. I will be notified, and then you'll
94             automatically be notified of progress on your bug as I make changes.
95              
96              
97             =head1 SUPPORT
98              
99             You can find documentation for this module with the perldoc command.
100              
101             perldoc Bio::Gonzales
102              
103              
104             You can also look for information at:
105              
106             =over 4
107              
108             =item * RT: CPAN's request tracker
109              
110             L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Gonzales>
111              
112             =item * AnnoCPAN: Annotated CPAN documentation
113              
114             L<http://annocpan.org/dist/Bio-Gonzales>
115              
116             =item * CPAN Ratings
117              
118             L<http://cpanratings.perl.org/d/Bio-Gonzales>
119              
120             =item * Search CPAN
121              
122             L<http://search.cpan.org/dist/Bio-Gonzales/>
123              
124             =back
125              
126              
127             =head1 ACKNOWLEDGEMENTS
128              
129              
130             =head1 LICENSE AND COPYRIGHT
131              
132             Copyright 2010 Joachim Bargsten.
133              
134             This program is free software; you can redistribute it and/or modify it
135             under the terms of either: the GNU General Public License as published
136             by the Free Software Foundation; or the Artistic License.
137              
138             See http://dev.perl.org/licenses/ for more information.
139              
140              
141             =cut
142              
143             1; # End of Bio::Gonzales