NAME

Bio::ViennaNGS::AnnoC - Perl extension for converting sequence annotation formats

SYNOPSIS

  use Bio::ViennaNGS::AnnoC;

  parse_gff($gff3_file);
  feature_summary($fstat,$dest);
  get_fasta_ids($fasta_file);

DESCRIPTION

parse_gff($gff3_file)

parse_gff() parses GFF3 annotation files. The GFF3 specification is available at http://www.sequenceontology.org/resources/gff3.html This routine expects the path to a GFF3 file as argument $gff3_file and returns two hash references: $feat is a reference to a HOH containing the raw annotation information for each feature found in the GFF3 file. $fstat references a hash containing summary statistics of the features found in the GFF3 file.

This routine has been tested with NCBI bacteria GFF3 annotation.

feature_summary($fstat,$dest)

This routine generates a summary file for all features parsed by parse_gff. It expects two arguments: $fstat is a refence to the summary hash generated by parse_gff() and $dest is the output path for a summary.txt file.

get_fasta_ids($fasta_file)

get_fasta_ids() returns an array containing all headers/IDs of a Fasta file as Bio::DB:Fasta objects. The Fasta file may contain multiple entries.

DEPENDENCIES

Bio::Tools::GFF

Bio::DB::Fasta

Path::Class

Carp

AUTHORS

Michael T. Wolfinger <michael@wolfinger.eu>

COPYRIGHT AND LICENSE

Copyright (C) 2014 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 5.12.4 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.