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

cpanm CracTools

perl -MCPAN -e shell
install CracTools