NAME

Bio::RNA::Treekin - Classes for working with Treekin output.

SYNOPSIS

    use Bio::RNA::Treekin;

    # Read multi-record file (records separated by single '&')
    my $treekin_records = Bio::RNA::Treekin::MultiRecord->new($treekin_file);

    # Iterate over single records.
    while (defined (my $next_treekin_record = $treekin_records->next)) {
        # Print current file name.
        print 'Treekin simulation for ', $next_treekin_record->rates_file, " \n";

        # Print population of minimum 42 at the end of the simulation
        my  $init_pop = $current_treekin_record->init_population;
        my $final_pop = $current_treekin_record->final_population;
        print 'min 42: ', $init_pop->of_min(42), ' => ',
              $final_pop->of_min(42), "\n";
    }

DESCRIPTION

This module provides auxiliary classes to parse, query and print the data generated by the reaction kinetics simulation tool Treekin, as well as multi-landscape simulations as generated by BarMap.

Both Treekin and BarMap are being developed by the Theoretical Biochemistry Group (TBI) of the University of Vienna. Note that this package is not developed or supported by the authors of Treekin and BarMap.

CLASSES

To process a regular output file of Treekin, use a record object as provided by Bio::RNA::Treekin::Record. When working with multi-record files as produced by BarMap, use a record stream from Bio::RNA::Treekin::MultiRecord to retrieve the individual simulation records.

Each Treekin record comprises, beside meta-information, a time series of populations of each minimum. These data are stored as objects of type Bio::RNA::Treekin::PopulationDataRecord.

Please refer to the documenation of the individual classes for more information.

AUTHOR

Felix Kuehnl, <felix@bioinf.uni-leipzig.de>

BUGS

Please report any bugs or feature requests by raising an issue at https://github.com/xileF1337/Bio-RNA-Treekin/issues.

You can also do so by mailing to bug-bio-rna-treekin at rt.cpan.org, or through the web interface at https://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-RNA-Treekin. 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::RNA::Treekin

You can also look for information at:

• Github: the official repository

  https://github.com/xileF1337/Bio-RNA-Treekin

• RT: CPAN's request tracker (report bugs here)

  https://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-RNA-Treekin

• AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/Bio-RNA-Treekin

• CPAN Ratings

  https://cpanratings.perl.org/d/Bio-RNA-Treekin

• Search CPAN

  https://metacpan.org/release/Bio-RNA-Treekin

LICENSE AND COPYRIGHT

Copyright 2019-2021 Felix Kuehnl.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.