File Coverage

blib/lib/Bio/RNA/Treekin.pm
Criterion Covered Total %
statement 14 14 100.0
branch n/a
condition n/a
subroutine 5 5 100.0
pod n/a
total 19 19 100.0


line stmt bran cond sub pod time code
1             # Bio/RNA/Treekin.pm
2             package Bio::RNA::Treekin;
3             our $VERSION = '0.05';
4              
5 4     4   351280 use 5.006;
  4         47  
6 4     4   24 use strict;
  4         7  
  4         99  
7 4     4   19 use warnings;
  4         6  
  4         102  
8              
9 4     4   2167 use Bio::RNA::Treekin::Record;
  4         15  
  4         220  
10 4     4   2978 use Bio::RNA::Treekin::MultiRecord;
  4         19  
  4         249  
11              
12             1;
13              
14             __END__
15              
16              
17             =pod
18              
19             =encoding UTF-8
20              
21             =head1 NAME
22              
23             Bio::RNA::Treekin - Classes for working with I<Treekin> output.
24              
25             =head1 SYNOPSIS
26              
27             use Bio::RNA::Treekin;
28              
29             # Read multi-record file (records separated by single '&')
30             my $treekin_records = Bio::RNA::Treekin::MultiRecord->new($treekin_file);
31              
32             # Iterate over single records.
33             while (defined (my $next_treekin_record = $treekin_records->next)) {
34             # Print current file name.
35             print 'Treekin simulation for ', $next_treekin_record->rates_file, " \n";
36              
37             # Print population of minimum 42 at the end of the simulation
38             my $init_pop = $current_treekin_record->init_population;
39             my $final_pop = $current_treekin_record->final_population;
40             print 'min 42: ', $init_pop->of_min(42), ' => ',
41             $final_pop->of_min(42), "\n";
42             }
43              
44             =head1 DESCRIPTION
45              
46             This module provides auxiliary classes to parse, query and print the data
47             generated by the reaction kinetics simulation tool I<Treekin>, as well as
48             multi-landscape simulations as generated by I<BarMap>.
49              
50             Both I<Treekin> and I<BarMap> are being developed by the Theoretical
51             Biochemistry Group (TBI) of the University of Vienna. Note that this
52             package is I<not> developed or supported by the authors of I<Treekin> and
53             I<BarMap>.
54              
55             =head1 CLASSES
56              
57             To process a regular output file of I<Treekin>, use a record object as
58             provided by L<Bio::RNA::Treekin::Record>. When working with multi-record files
59             as produced by I<BarMap>, use a record stream from
60             L<Bio::RNA::Treekin::MultiRecord> to retrieve the individual simulation
61             records.
62              
63             Each I<Treekin> record comprises, beside meta-information, a time series of
64             populations of each minimum. These data are stored as objects of type
65             C<Bio::RNA::Treekin::PopulationDataRecord>.
66              
67             Please refer to the documenation of the individual classes for more
68             information.
69              
70             =head1 AUTHOR
71              
72             Felix Kuehnl, C<< <felix@bioinf.uni-leipzig.de> >>
73              
74              
75             =head1 BUGS
76              
77             Please report any bugs or feature requests by raising an issue at
78             L<https://github.com/xileF1337/Bio-RNA-Treekin/issues>.
79              
80             You can also do so by mailing to C<bug-bio-rna-treekin at rt.cpan.org>,
81             or through the web interface at
82             L<https://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-RNA-Treekin>. I will be
83             notified, and then you'll automatically be notified of progress on your bug as
84             I make changes.
85              
86              
87             =head1 SUPPORT
88              
89             You can find documentation for this module with the perldoc command.
90              
91             perldoc Bio::RNA::Treekin
92              
93              
94             You can also look for information at:
95              
96             =over 4
97              
98             =item * Github: the official repository
99              
100             L<https://github.com/xileF1337/Bio-RNA-Treekin>
101              
102             =item * RT: CPAN's request tracker (report bugs here)
103              
104             L<https://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-RNA-Treekin>
105              
106             =item * AnnoCPAN: Annotated CPAN documentation
107              
108             L<http://annocpan.org/dist/Bio-RNA-Treekin>
109              
110             =item * CPAN Ratings
111              
112             L<https://cpanratings.perl.org/d/Bio-RNA-Treekin>
113              
114             =item * Search CPAN
115              
116             L<https://metacpan.org/release/Bio-RNA-Treekin>
117              
118             =back
119              
120              
121             =head1 LICENSE AND COPYRIGHT
122              
123             Copyright 2019-2021 Felix Kuehnl.
124              
125             This program is free software: you can redistribute it and/or modify
126             it under the terms of the GNU General Public License as published by
127             the Free Software Foundation, either version 3 of the License, or
128             (at your option) any later version.
129              
130             This program is distributed in the hope that it will be useful,
131             but WITHOUT ANY WARRANTY; without even the implied warranty of
132             MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
133             GNU General Public License for more details.
134              
135             You should have received a copy of the GNU General Public License
136             along with this program. If not, see L<http://www.gnu.org/licenses/>.
137              
138              
139             =cut
140              
141             # End of Bio/RNA/Treekin.pm
142