/ 
Bio-RNA-Barriers-0.03
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/ Bio::RNA::Barriers::Results

NAME

Bio::RNA::Barriers::Results - Parse, query and manipulate results of a Barriers run

SYNOPSIS

use Bio::RNA::Barriers;

# Read in a Barriers output file.
open my $barriers_handle, '<', $barriers_file;
my $bardat = Bio::RNA::Barriers::Results->new($barriers_handle);
# Or, even simpler, pass file name directly:
$bardat    = Bio::RNA::Barriers::Results->new($barriers_file  );

# Print some info
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;
print "Min ", $min3->index, " is ", ($min3->is_connected ? "" : "NOT"),
      " connected to the mfe structure.\n";

# Print the mfe basin line as in the results file
my $mfe_min = $bardat->get_global_min();
print "$mfe_min\n";

DESCRIPTION

This is what you usually want to use. Pass a file name or a handle to the constructor and you're golden. When querying a specific minimum by index, a Bio::RNA::Barriers::Minimum object is returned. For more details on its methods, please refer to its documentation.

METHODS

Bio::RNA::Barriers::Results->new()

Constructs the results object from a Barriers results file.

Supported argument list types:
new($barriers_file_path):

Open handle and read data from the passed path, set file name accordingly.

new($barriers_handle):

A file handle to read data from, file_name() will return undef.

new($barriers_handle, $barriers_file_path):

Read data from handle and set file name from a given path.

new($hash_ref):

Manual construction from required attributes. Only for experts.

$res->seq()

Returns the RNA sequence for which the minima have been computed.

$res->file_name()

Name of the file from which the minima have been read. May be undef.

$res->mins()

Returns a list of all minima. Useful for iteration in for loops.

$res->get_min($index)

Return the single minimum given by a 1-based $index (as used in the results file).

$res->get_mins(@indices)

Return a list of minima given by a 1-based list of @indices (as used in the results file).

$res->get_global_min()

Returns the basin represented by the (global) mfe structure (i.e. basin 1).

$res->mfe()

Get the global minimum free energy.

$res->delta_energy()

Get the delta_E of the landscape, i. e. the energy difference between the (global) minimum free energy and and the highest energy encountered.

$res->max_energy()

Get the maximum energy of any structure in the landscape.

$res->min_count()

Returns the total number of basins.

$res->connected_mins()

Returns a list of all minima connected to the mfe minimum (min 1).

$res->connected_indices()

Returns a list of indices of all connected minima (cf. connected_mins()).

$res->keep_connected()

Keep only connected minima and remove all others. The indices are remapped to 1..k for k kept minima. Returns (old) indices of all kept minima.

$res->update_connected(@connected_mins)

Given an ordered list of indices of all connected minima (as returned by RateMatrix::keep_connected()), delete all other minima and update their ancesters' basin size information accordingly.

$res->keep_first_mins($min_count)

Keep only the first $min_count mins. (If there are only that many or less minima in total, do nothing.)

WARNING: THIS CAN DISCONNECT THE LANDSCAPE! The bar file will still look connected, however, modifying the rate matrix accordingly can lead to non-ergodicity (e.g. when basin 3 merged to 2, 2/3 merged to 1 because of a possible transition from 3 to 1, and basin 3 is then removed). Returns a list of all removed mins (may be empty).

$res->has_bsize()

Check whether the stored minima contain information about the basin sizes as computed by Barriers' --bsize switch. Checks only the mfe basin (since all or neither min should have this information).

$res->path()

Construct the file path to this Barriers file. Works only if it was actually parsed from a file (of course...). Returns the path as a string.

$res->stringify()

Convert back to Barriers file. Also supports stringification overloading, i. e. "$res" is equivalent to $res->stringify().

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/

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/.