CracTools::Interval::Query::File - Acts like CracTools::Interval::Query but read interval from files and return lines of the file matching the query.
version 1.24
Add an otpion that gives an method wich can parsed the return line.
Arg [file] : String - file path Arg [type] : String - file type (bed,sam,gff,gtf) Example : my $gffQuery = CracTools::GFF::Query->new('annotations.gff'); Description : Create a new GFF Query object ReturnType : CracTools::GFF::Query Exceptions : none
Return an array reference of intervals associated with the line.
Interval structure is described by get_interval_sub
Return a line of a file at a give seek position.
$self->_processReturnValue($val)
Overload _processReturnValue() method to retrieve lines from files using seek positions.
Interval must be : 1-base coordinate system Closed intervals
We transform BED annotation postions to base-1 positions, and closed intervals
Nicolas PHILIPPE <nphilippe.research@gmail.com>
Jérôme AUDOUX <jaudoux@cpan.org>
Sacha BEAUMEUNIER <sacha.beaumeunier@gmail.com>
This software is Copyright (c) 2016 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.