/ 
CracTools-1.08
River stage one • 1 direct dependent • 1 total dependent
/ CracTools::Interval::Query

NAME

CracTools::Interval::Query - Query intervals in various type of files

VERSION

version 1.08

new

Arg [1] : String - GFF file

Example     : my $gffQuery = CracTools::GFF::Query->new('annotations.gff');
Description : Create a new GFF Query object
ReturnType  : CracTools::GFF::Query
Exceptions  : none

fetchByRegion

Arg [1] : String $seq_region_name
          The name of the sequence region that the slice will be
          created on.
Arg [2] : int $start
          The start of the slice on the sequence region
Arg [3] : int $end
          The end of the slice on the sequence region
Arg [4] : int $strand
          The orientation of the slice on the sequence region
Arg [5] : (Optional) Boolean $windowed
          Only return lines whose intervals are completely contained
          if the slide.

Example     : my @lines = $IntervalQuery->fetchByRegion('1',298345,309209,'+');
Description : Retrives lines that belong to the region.
ReturnType  : Reference to an Array of strings
Exceptions  : none

fetchByLocation

Arg [1] : String $seq_region_name
          The name of the sequence region that the slice will be
          created on.
Arg [2] : int $position
          Location to look for
Arg [3] : int $strand
          The orientation of the slice on the sequence region

Example     : my @lines = $intervalQuery->fetchByLocation('1',298345,'+');
Description : Retrives lines that overlapped the given location.
ReturnType  : Reference to an Array of strings
Exceptions  : none

fetchNearestDown

Search for the closest interval in downstream that does not contain the query and returns the line associated to this interval.

fetchAllNearestDown

Search for the closest intervals in downstream that does not contain the query and returns an array reference of lines associated to these intervals.

fetchNearestUp

Search for the closest interval in downstream that does not contain the query and returns the line associated to this interval.

fetchAllNearestUp

Search for the closest intervals in downstream that does not contain the query and returns an array reference of lines associated to these intervals.

_getIntervals

Return an array reference of intervals associated with the line.

Interval structure is described by get_interval_sub

_getLine

_getLines

_getIntervalTree

$self->getIntervalTree($chr,$strand);

Return the interval tree reference for the chromosome and strand

_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 <nicolas.philippe@inserm.fr>

  • Jérôme AUDOUX <jaudoux@cpan.org>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2014 by IRB/INSERM (Institut de Recherche en Biothérapie / Institut National de la Santé et de la Recherche Médicale).

This is free software, licensed under:

CeCILL FREE SOFTWARE LICENSE AGREEMENT, Version 2.1 dated 2013-06-21