NAME

Bio::RNA::Barriers - Parse, query and manipulate output of Barriers

SYNOPSIS

    use Bio::RNA::Barriers;

    ##### Working with the Barriers results file (*.bar) #####
    $bardat = Bio::RNA::Barriers::Results->new('bar_file.bar');

    print "There are ", $bardat->min_count, " minima.";

    my $min3 = $bardat->get_min(3);
    print $min3->grad_struct_count,
          " structures lead to basin 3 via a gradient walk.\n"
        if $min3->has_bsize;

    my $mfe_min = $bardat->get_global_min();
    print "$mfe_min\n";             # prints minimum as in the results file


    ##### Working with the rate matrix files (rates.{out,bin}) #####
    my $rate_matrix = Bio::RNA::Barriers::RateMatrix->new(
        file_name => '/path/to/rates.bin',
        file_type => 'BIN',
    );

    print "$rate_matrix";               # prints entire matrix in text format
    print 'Dimension of rate matrix is ', $rate_matrix->dim, "\n";
    print 'Rate from state 1 to state 3 is ',
          $rate_matrix->rate_from_to(1, 3),
          "\n";

    $rate_matrix->remove_states(1, 5, 5, 3);    # state 2 becomes state 1 etc.
    $rate_matrix->keep_states(1..3);            # keep only states {1, 2, 3}.
    $rate_matrix->keep_connected();             # remove disconnected states

    open my $out_fh_bin, '>', '/path/to/output/rates.bin';
    $rate_matrix->print_as_bin($out_fh_bin);    # write binary output

DESCRIPTION

This module provides auxiliary classes to parse, query, manipulate and print the files generated by Barriers, a tool to compute RNA energy landscapes and folding kinetics developed at Theoretical Biochemistry Group (TBI) at the University of Vienna. Note that this module is not written and maintained by the authors of Barriers.

Supports the result file (written to STDOUT by Barriers) as well as rate matrices in binary and text format. Properties like the number of minima or, for each minima, their fathers and children, connectedness, and basin sizes can be queried.

Rate matrices can be manipulated easily, e. g. to remove or keep certain states or to convert between binary and text representation.

CLASSES

This module provides two major classes to handle the results: Bio::RNA::Barriers::Results and Bio::RNA::Barriers::Minimum, where the first is an aggregate results object containing objects from the second. Usually you want to pass a file name or handle to a Barriers file to the constructor of the results class (i. e., Bio::RNA::Barriers::Results->new()), and the rest is taken care of automatically.

For rate matrices, Bio::RNA::Barriers::RateMatrix is provided. It can parse both text and binary matrices. Make sure to correctly set the file type argument when passing the path or handle to the constructor.

For a description of the available methods, please refer to the documentation of each individual class, i. e. run perldoc Bio::RNA::Barriers::Results etc.

AUTHOR

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

BUGS

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

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

You can also look for information at the official Barriers website:

https://www.tbi.univie.ac.at/RNA/Barriers/

• Github: the official repository

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

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

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

• AnnoCPAN: Annotated CPAN documentation

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

• CPAN Ratings

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

• Search CPAN

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

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/.