Jérôme Audoux
and 2 contributors

NAME

CracTools::Interval::Query::File - Acts like CracTools::Interval::Query but read interval from files and return lines of the file matching the query.

VERSION

version 1.251

TODO

Add an otpion that gives an method wich can parsed the return line.

new

  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

_getIntervals

Return an array reference of intervals associated with the line.

Interval structure is described by get_interval_sub

_getLine

Return a line of a file at a give seek position.

_processReturnValue

  $self->_processReturnValue($val)

Overload _processReturnValue() method to retrieve lines from files using seek positions.

_getIntervalsFrom<FORMAT>Line

Interval must be : 1-base coordinate system Closed intervals

_getIntervalsFromBEDLine

We transform BED annotation postions to base-1 positions, and closed intervals

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