CracTools::GFF::Annotation - Parse GFF lines.
version 1.251
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"; }
This module defines an object to easily parse and access GFF line's fields.
Set Parent for feature in GTF format (gene_id for transcript and transcript_id for exons).
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
Description : Getter/setter for attribute chr
Description : Getter/setter for attribute source
Description : Getter/setter for attribute feature
Description : Getter/setter for attribute start
Description : Getter/setter for attribute end
Description : Getter/setter for attribute score
Description : Getter/setter for attribute strand ('1','-1' convention)
Description : Return strand using "+","-" convention.
Description : Getter/setter for attribute phase
Description : Getter for attribute parents. ReturnType : Array of strings with parents ID
Description : Getter/setter for attribute attribute
Nicolas PHILIPPE <nphilippe.research@gmail.com>
Jérôme AUDOUX <jaudoux@cpan.org>
Sacha BEAUMEUNIER <sacha.beaumeunier@gmail.com>
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
To install CracTools, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CracTools
CPAN shell
perl -MCPAN -e shell install CracTools
For more information on module installation, please visit the detailed CPAN module installation guide.