NAME

Bio::ViennaNGS::AnnoC - Object-oriented interface for storing and converting biological sequence annotation formats

SYNOPSIS

use Bio::ViennaNGS::AnnoC;

my $obj = Bio::ViennaNGS::AnnoC->new();

# parse GFF3 file to internal data straucture
$obj->parse_gff($gff3_file);

# compute summary of parsed annotation
$obj->featstat;

# dump feature summary to file
$obj->feature_summary($dest);

# dump all tRNAs contained in data structure as BED12
$obj->features2bed("tRNA",$dest,$bn,$log)

DESCRIPTION

This module provides an object-oriented interface for storing and converting biological sequence annotation data. Based on the Moose object system, it maintains a central data structure which is curently designed to represent simple, non-spliced (ie single-exon) annotation data. Future versions of the module will account for more generic scenarios, including spliced isoforms.

METHODS

parse_gff

Title : parse_gff Usage : <$obj-parse_gff($gff3_file);>> Function: Parses GFF3 annotation files of non-spliced genomes into <$self-features>> Args : The full path to a GFF3 file Returns : Notes : The GFF3 specification is available at http://www.sequenceontology.org/resources/gff3.html. This routine has been tested with NCBI bacteria GFF3 annotation.

feature_summary

Title : feature_summary Usage : <$obj-feature_summary($dest);>> Function : Generate a summary file for all features present in <$self-features>> Args : Full output path for summary.txt file Returns :

features2bed

Title : features2bed Usage : <$obj-features2bed($feature,$workdir,$bn,$log);>> Function : Dumps genomic features from $self-features> hash to a BED12 file. Args : <$gbkey> can be either a string corresponding to a genbank key in <$self-featstat>> or undef. If defined, only features of the speficied key will be dumped to a single BED12 file. If $gbkey is undef, BED12 files will be generated for each type present in <$self-featstat>>. $dest is the output directory and $bn the basename for all output files. $log is either be the full path to a logfile or undef. Returns :

DEPENDENCIES

Bio::Tools::GFF

IPC::Cmd

Path::Class

Carp

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.