Bio::ViennaNGS::AnnoC - Object-oriented interface for storing and converting biological sequence annotation formats
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)
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.
Moose
Title : parse_gff
Usage : $obj->parse_gff($gff3_file);
$obj->parse_gff($gff3_file);
Function: Parses GFF3 annotation files of non-spliced genomes into $self->features
$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.
Title : feature_summary
Usage : $obj->feature_summary($dest);
$obj->feature_summary($dest);
Function : Generate a summary file for all features present in $self->features
Args : Full output path for summary.txt file
Title : features2bed
Usage : $obj->features2bed($feature,$workdir,$bn,$log);
$obj->features2bed($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.
$gbkey
$self->featstat
undef
$dest
$bn
$log
Michael T. Wolfinger <michael@wolfinger.eu>
Copyright (C) 2014-2017 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.
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ViennaNGS
CPAN shell
perl -MCPAN -e shell install Bio::ViennaNGS
For more information on module installation, please visit the detailed CPAN module installation guide.