annotate variant_effect_predictor/Bio/EnsEMBL/Variation/StructuralVariationOverlapAllele.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
author devteam <devteam@galaxyproject.org>
date Mon, 13 Jan 2014 10:38:30 -0500
parents 1f6dce3d34e0
children
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1 package Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;
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2
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3 use strict;
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4 use warnings;
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6 use base qw(Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele);
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8 sub new_fast {
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9 my ($class, $hashref) = @_;
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11 # swap a transcript_variation argument for a variation_feature_overlap one
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13 if ($hashref->{structural_variation_overlap}) {
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14 $hashref->{base_variation_feature_overlap} =
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15 delete $hashref->{structural_variation_overlap};
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16 }
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18 # and call the superclass
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20 return $class->SUPER::new_fast($hashref);
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21 }
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23 =head2 structural_variation_overlap
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25 Description: Get the associated StructuralVariationOverlap
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26 Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlap
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27 Exceptions : none
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28 Status : At Risk
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30 =cut
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32 sub structural_variation_overlap {
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33 my ($self, $svo) = @_;
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34 if ($svo) {
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35 assert_ref($svo, 'Bio::EnsEMBL::Variation::StructuralVariationOverlap');
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36 }
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37 return $self->base_variation_feature_overlap($svo);
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38 }
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41 =head2 structural_variation_feature
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42
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43 Description: Get the associated StructuralVariationFeature
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44 Returntype : Bio::EnsEMBL::Variation::StructuralVariationFeature
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45 Exceptions : none
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46 Status : At Risk
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47
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48 =cut
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50 sub structural_variation_feature {
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51 my $self = shift;
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52 return $self->structural_variation_overlap->structural_variation_feature;
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53 }
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55 1;
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