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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 =head1 SYNOPSIS
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24
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25 =head1 DESCRIPTION
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26
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27 =head1 METHODS
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28
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29 =cut
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30
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31 package Bio::EnsEMBL::Utils::VegaCuration::Gene;
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32
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33 use strict;
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34 use warnings;
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35 use vars qw(@ISA);
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36
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37 use Bio::EnsEMBL::Utils::ConversionSupport;
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38
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39 @ISA = qw(Bio::EnsEMBL::Utils::ConversionSupport);
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40
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41
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42 =head2 find_gaps
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43
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44 Args : arrayref of B::E::Transcripts
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45 Example : my $gaps = find_gaps($all_transcripts)
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46 Description: identifies regions of a gene that are not covered by any transcript
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47 Returntype : int
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48 Exceptions : none
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49 Caller : internal
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50
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51 =cut
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52
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53 sub find_gaps {
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54 my $self = shift;
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55 my ($all_transcripts) = @_;
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56 my $gaps = 0;
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57 my @sorted_transcripts = sort {$a->start <=> $b->start || $b->end <=> $a->end} @{$all_transcripts};
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58 if ( my $first_transcript = shift @sorted_transcripts ) {
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59 my $pos = $first_transcript->end;
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60 foreach my $transcript (@sorted_transcripts) {
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61 next if ($transcript->end < $pos );
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62 if ($transcript->start < $pos && $transcript->end > $pos ) {
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63 $pos = $transcript->end;
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64 next;
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65 }
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66 elsif ($transcript->end > $pos) {
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67 $gaps++;
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68 $pos = $transcript->end;
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69 }
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70 }
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71 }
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72 return $gaps;
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73 }
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