Joachim Bargsten > Bio-Gonzales > Bio::Gonzales::Range::Overlap

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Module Version: 0.0549   Source  

NAME ^

Bio::Gonzales::Range::Overlap - find overlapping ranges

SYNOPSIS ^

  use 5.010;
  use Bio::Gonzales::Range::Overlap;
  use Data::Dumper;

  my @ranges1 = (
    [ 0, 5, 'some', 'information' ],
    [ 6, 8,  'some',     'other', 'information' ],
    [ 7, 10, 'nonsense', 'information' ],
    [ 11, 100, { 'very' => 'complicated', "data" => 'structure' } ],
  );

  my $ro = Bio::Gonzales::Range::Overlap->new;

  #build query db from 1st set of intervals
  for my $r (@ranges1) {
    $ro->insert(@$r);
  }

  # in this case (from and to are elements 0 and 1)
  # insert could be called with all ranges
  #$ro->insert(\@ranges1);

  my @ranges2 = ( [ 8, 10 ], [ 1, 3 ], [99,200],);

  # query the db with ranges
  for my $r (@ranges2) {
    say "Range (" . join(",", @$r) . ") overlaps with:";
    say Dumper $ro->overlaps_with(@$r);
  }

DESCRIPTION ^

A @range has the form ($from, $to, @additional elements). Lists of ranges have the form ([$from, $to, @add_elems], [$from, $to, @add_elems], ...).

OPTIONS ^

METHODS ^

$ro->insert(@range)
$ro->insert(\@list_of_ranges)
\@ranges_contained_in_given_range = $ro->contained_in(@range)
\@ranges_that_overlap_with_given_range = $ro->overlaps_with(@range)

SEE ALSO ^

Bio::Gonzales::Matrix::IO for reading in ranges from files
Bio::Gonzales::Range::GroupedOverlap for grouped ranges such as genes that are grouped by chromosomes.

AUTHOR ^

jw bargsten, <jwb at cpan dot org>

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