NAME
Bio::ViennaNGS::FeatureIO - Versatile I/O interface for Bio::ViennaNGS feature annotation classes
SYNOPSIS
use Bio::ViennaNGS::FeatureIO;
# create a new object and parse the contents of a bedGraph file
my $obj = Bio::ViennaNGS::FeatureIO->new(file => "file.bg",
filetype => "BedGraph",
objecttype => "BedGraph",
);DESCRIPTION
This module provides an object-oriented interface for easy input/output operations on common feature annotation file formats. It is - by design - a very generic module that stores all annotation data within the $self->data ArrayRef. $self->objecttype determines the type of elements in $self->data.
Currently parsing of bedGraph files into an array of Bio::ViennaNGS::BedGraphEntry objects is supported.
METHODS
- parse_bedgraph_file
-
Title : parse_gff
Usage :
$obj->parse_bedgraph_file($bedgraph_file);Function: Parses bedGraph coverage data into
$self->data.Args : The full path to a bedGraph file
Returns : Nothing.
Notes : The bedGraph specification is available at http://genome.ucsc.edu/goldenpath/help/bedgraph.html.
DEPENDENCIES
AUTHORS
Michael T. Wolfinger <michael@wolfinger.eu>
COPYRIGHT AND LICENSE
Copyright (C) 2014-2015 Michael T. Wolfinger <michael@wolfinger.eu>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.
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.