NAME

CracTools::GFF::Annotation - Parse GFF lines.

VERSION

version 1.251

SYNOPSIS

  use CracTools::GFF::Query;

  # Creating the reader
  my $gffQuery = CracTools::GFF::Query->new('annotations.gff');

  my @annotations = $gffQuery->fetchByLocation('1',298345,'+');

  foreach my $gff_line (@annotations) {
    my $annotation = CracTools::GFF::Annotation->new($gff_line);
    print "Gene_id : ",$annotation->attribute('gene_id'),"\n";
  }

DESCRIPTION

This module defines an object to easily parse and access GFF line's fields.

TODO

Set Parent for feature in GTF format (gene_id for transcript and transcript_id for exons).

METHODS

new

  Arg [1] : String - $line
            GFF line
  Arg [2] : String - $format (optional) - default 'gff3'
            GFF format (gtf or gff3)

  Example     : my $annotation = CracTools::GFF::Annotation->new($gff_line);
  Description : Create a new CracTools::GFF::Annotation object
                If a gff line is passed in argument, the line will be parsed
                and loaded.
  ReturnType  : CracTools::GFF::Query

GETTERS AND SETTERS

chr

  Description : Getter/setter for attribute chr

source

  Description : Getter/setter for attribute source

feature

  Description : Getter/setter for attribute feature

start

  Description : Getter/setter for attribute start

end

  Description : Getter/setter for attribute end

score

  Description : Getter/setter for attribute score

strand

  Description : Getter/setter for attribute strand ('1','-1' convention)

gffStrand

  Description : Return strand using "+","-" convention.

phase

  Description : Getter/setter for attribute phase

parents

  Description : Getter for attribute parents.
  ReturnType  : Array of strings with parents ID

attribute

  Description : Getter/setter for attribute attribute

AUTHORS

  • Nicolas PHILIPPE <nphilippe.research@gmail.com>

  • Jérôme AUDOUX <jaudoux@cpan.org>

  • Sacha BEAUMEUNIER <sacha.beaumeunier@gmail.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2017 by IRMB/INSERM (Institute for Regenerative Medecine and Biotherapy / Institut National de la Santé et de la Recherche Médicale) and AxLR/SATT (Lanquedoc Roussilon / Societe d'Acceleration de Transfert de Technologie).

This is free software, licensed under:

  The GNU Affero General Public License, Version 3, November 2007