Raw content of Bio::EnsEMBL::Utils::VegaCuration::Gene
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::VegaCuration::Gene;
use strict;
use warnings;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::ConversionSupport;
@ISA = qw(Bio::EnsEMBL::Utils::ConversionSupport);
=head2 find_gaps
Args : arrayref of B::E::Transcripts
Example : my $gaps = find_gaps($all_transcripts)
Description: identifies regions of a gene that are not covered by any transcript
Returntype : int
Exceptions : none
Caller : internal
=cut
sub find_gaps {
my $self = shift;
my ($all_transcripts) = @_;
my $gaps = 0;
my @sorted_transcripts = sort {$a->start <=> $b->start || $b->end <=> $a->end} @{$all_transcripts};
my $first_transcript = shift @sorted_transcripts;
my $pos = $first_transcript->end;
foreach my $transcript (@sorted_transcripts) {
next if ($transcript->end < $pos );
if ($transcript->start < $pos && $transcript->end > $pos ) {
$pos = $transcript->end;
next;
}
elsif ($transcript->end > $pos) {
$gaps++;
$pos = $transcript->end;
}
}
return $gaps;
}
]]>