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package Sanger::CGP::Vagrent::Annotators::DeletionAnnotator; |
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##########LICENCE########## |
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# Copyright (c) 2014-2017 Genome Research Ltd. |
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# |
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# Author: Cancer Genome Project cgpit@sanger.ac.uk |
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# |
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# This file is part of VAGrENT. |
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# |
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# VAGrENT is free software: you can redistribute it and/or modify it under |
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# the terms of the GNU Affero General Public License as published by the Free |
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# Software Foundation; either version 3 of the License, or (at your option) any |
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# later version. |
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# |
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# This program is distributed in the hope that it will be useful, but WITHOUT |
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
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# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more |
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# details. |
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# |
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# You should have received a copy of the GNU Affero General Public License |
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# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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##########LICENCE########## |
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use strict; |
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use Bio::Seq; |
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use Carp qw(cluck); |
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use Log::Log4perl; |
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use POSIX qw(ceil); |
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use Data::Dumper; |
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use Sanger::CGP::Vagrent::Data::Deletion; |
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use Sanger::CGP::Vagrent qw($VERSION); |
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use base qw(Sanger::CGP::Vagrent::Annotators::AbstractAnnotator); |
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my $log = Log::Log4perl->get_logger(__PACKAGE__); |
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1; |
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sub _getAnnotation { |
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my ($self,$var) = @_; |
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$self->_clearMessages(); |
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unless(defined($var) && $var->isa('Sanger::CGP::Vagrent::Data::Deletion')){ |
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my $msg = 'require a Sanger::CGP::Vagrent::Data::Deletion object not a '.ref($var); |
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$self->addMessage($msg); |
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$log->info($msg); |
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return undef; |
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} |
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unless($var->isValid){ |
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my $msg = 'deletion not valid'; |
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$self->addMessage($msg); |
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$log->error($msg); |
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return undef; |
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} |
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my @trans = $self->_getTranscriptSource->getTranscripts($var); |
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unless(defined($trans[0])){ |
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my $msg = 'No transcripts returned from transcript source'; |
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$self->addMessage($msg); |
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$log->info($msg); |
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return undef; |
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} |
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my @groups; |
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foreach my $t(@trans){ |
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my $g = $self->_generateAnnotatonGroup($var,$t); |
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if(defined($g)){ |
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push(@groups,$g); |
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} |
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} |
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unless(scalar(@groups) > 0 && defined($groups[0])){ |
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my $msg = 'No annotation groups generated'; |
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$self->addMessage($msg); |
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$log->info($msg); |
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return undef; |
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} |
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return @groups; |
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} |
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sub _generateAnnotatonGroup { |
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my ($self,$var,$tran) = @_; |
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my ($rAnnot,@groupClasses) = $self->_buildRNAAnnotation($var,$tran); |
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@groupClasses = sort @groupClasses; |
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unless(defined($rAnnot)){ |
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my $msg = 'No mRNA annotation created'; |
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$self->addMessage($msg); |
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$log->info($msg); |
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return undef; |
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} |
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my $group = Sanger::CGP::Vagrent::Data::AnnotationGroup->new( accession => $tran->getAccession, |
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label => $tran->getGeneName, |
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ccds => $tran->getCCDS, |
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type => $tran->getGeneType,); |
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if($tran->isProteinCoding){ |
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if( ( $rAnnot->hasClassification($self->getIntronVariantClass) || |
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$rAnnot->hasClassification($self->get5KBUpStreamVariantClass) || |
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$rAnnot->hasClassification($self->get2KBUpStreamVariantClass) || |
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$rAnnot->hasClassification($self->get5KBDownStreamVariantClass) || |
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$rAnnot->hasClassification($self->get500BPDownStreamVariantClass)) && |
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!$rAnnot->hasClassification($self->getEssentialSpliceSiteVariantClass) && |
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!$rAnnot->hasClassification($self->getSpliceRegionVariantClass) && |
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!$rAnnot->hasClassification($self->getFrameShiftVariantClass) && |
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!$rAnnot->hasClassification($self->getInFrameVariantClass) && |
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!$rAnnot->hasClassification($self->get5PrimeUtrVariantClass) && |
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!$rAnnot->hasClassification($self->get3PrimeUtrVariantClass) && |
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!$rAnnot->hasClassification($self->getComplexChangeVariantClass)){ |
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# Inronic or up/down stream mutations don't need to get any further annotation |
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$group->addAnnotation($rAnnot); |
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} else { |
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my $cAnnot = $self->_buildCDSAnnotation($var,$tran,$rAnnot); |
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unless(defined($cAnnot)){ |
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my $msg = 'No CDS annotation created'; |
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$self->addMessage($msg); |
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$log->info($msg); |
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return undef; |
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} |
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my $pAnnot = $self->_buildProteinAnnotation($var,$tran,$cAnnot,$rAnnot); |
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unless(defined($pAnnot)){ |
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my $msg = 'No Protein annotation created'; |
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$self->addMessage($msg); |
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$log->info($msg); |
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return undef; |
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} |
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$group->addAnnotation($rAnnot); |
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$group->addAnnotation($cAnnot); |
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$group->addAnnotation($pAnnot); |
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} |
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} else { |
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$group->addAnnotation($rAnnot); |
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} |
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$group->addClassification(@groupClasses); |
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return $group; |
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} |
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sub _buildRNAAnnotation { |
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my ($self,$var,$tran) = @_; |
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my ($mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset) = $self->_getmRNAPositions($var,$tran); |
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unless(defined($mrnaMin) && defined($mrnaMinOffset) && defined($mrnaMax) && defined($mrnaMaxOffset)){ |
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my $msg = 'problem generating mrna coordinates'; |
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$self->addMessage($msg); |
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$log->error($msg); |
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return undef; |
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} |
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unless($self->_safetyCheck($var,$tran,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset)){ |
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# something has gone wrong, |
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my $msg = 'The affected transcript WT sequence in the deleted sequence doesnt match the affected transcript WT sequence from the transcript'; |
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$self->addMessage($msg); |
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$log->error($msg); |
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return undef; |
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} |
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my @classes = ($self->getDeletionClass); |
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my @groupClasses = ($self->classifyTranscript($tran)); |
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my $upstream = $self->_upstreamVariantCheck($mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset,\@classes); |
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if(defined $upstream){ |
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if($upstream){ |
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return ($self->_buildUnknownMRNAAnnotation($var,$tran,@classes),@groupClasses); |
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} |
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} else { |
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return undef; |
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} |
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my $downstream = $self->_downstreamVariantCheck($mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset,\@classes); |
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if(defined $downstream){ |
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if($downstream){ |
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return ($self->_buildUnknownMRNAAnnotation($var,$tran,@classes),@groupClasses); |
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} |
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} else { |
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return undef; |
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} |
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# delt with up/down stream issues, can reset coordinates to the extremes of the transcript; |
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if($mrnaMin == 0 && $mrnaMinOffset <= 0){ |
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$mrnaMin = 1; |
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$mrnaMinOffset = 0; |
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} |
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if($mrnaMax == 0 && $mrnaMaxOffset >= 0){ |
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$mrnaMax = length($tran->getcDNASeq); |
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$mrnaMaxOffset = 0; |
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} |
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if($tran->isProteinCoding){ |
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if(($mrnaMax > $tran->getCdsMinPos || ($mrnaMax == $tran->getCdsMinPos && $mrnaMaxOffset >= 0)) && |
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($mrnaMin < $tran->getCdsMaxPos || ($mrnaMin == $tran->getCdsMaxPos && $mrnaMinOffset <= 0))){ |
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#if($mrnaMax >= $tran->getCdsMinPos && $mrnaMin <= $tran->getCdsMaxPos){ |
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# coding change |
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push(@groupClasses,$self->getCDSClass); |
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} |
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if($mrnaMin < $tran->getCdsMinPos || ($mrnaMin == $tran->getCdsMinPos && $mrnaMinOffset < 0)){ |
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#if($mrnaMin < $tran->getCdsMinPos){ |
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# 5prime UTR |
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push(@groupClasses,$self->get5PrimeUtrClass); |
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push(@classes,$self->get5PrimeUtrVariantClass) unless($self->_arrayHasString($self->getCDSClass,@groupClasses)); |
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} |
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if($mrnaMax > $tran->getCdsMaxPos || ($mrnaMax == $tran->getCdsMaxPos && $mrnaMaxOffset > 0)){ |
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#if($mrnaMax > $tran->getCdsMaxPos){ |
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# 3prime UTR |
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push(@groupClasses,$self->get3PrimeUtrClass); |
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push(@classes,$self->get3PrimeUtrVariantClass) unless($self->_arrayHasString($self->getCDSClass,@groupClasses)); |
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} |
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} |
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my $tmpGroupClassesHash = $self->_classifyDeletion($tran,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset); |
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push(@groupClasses, keys %$tmpGroupClassesHash); |
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if(scalar(keys %$tmpGroupClassesHash) == 1 && defined($tmpGroupClassesHash->{$self->getIntronClass})){ |
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# its intron only |
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return ($self->_buildUnknownMRNAAnnotation($var,$tran,$self->getDeletionClass,$self->getIntronVariantClass),@groupClasses); |
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} |
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my $wt = $self->_getWildTypeStringForRNAAnno($var,$tran); |
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my $mt = '-'; |
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$wt =~ tr/Tt/Uu/; |
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my $desc = undef; |
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if($mrnaMin == 1 && $mrnaMax == length($tran->getcDNASeq)){ |
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$desc = 'r.0'; |
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} else { |
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$desc = $self->_generateDNADelDescriptionString('r.',$mrnaMin,$mrnaMax,$mrnaMinOffset,$mrnaMaxOffset,$wt); |
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} |
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my $subtype = undef; |
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if($mrnaMin == 0 && $mrnaMax == 0){ |
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$subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffSequenceSubtype(); |
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} elsif($mrnaMinOffset == 0 && $mrnaMaxOffset == 0){ |
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$subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionKnownSubtype(); |
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} else { |
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$subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffsetSubtype(); |
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} |
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my $anno = Sanger::CGP::Vagrent::Data::Annotation->new( wt => uc($wt), |
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mt => $mt, |
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minpos => $mrnaMin, |
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minOffset => $mrnaMinOffset, |
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maxpos => $mrnaMax, |
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maxOffset => $mrnaMaxOffset, |
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acc => $tran->getAccession, |
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accversion => $tran->getAccessionVersion, |
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db => $tran->getDatabase, |
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dbversion => $tran->getDatabaseVersion, |
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seqlength => length($tran->getcDNASeq), |
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description => $desc, |
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context => Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext(), |
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type => Sanger::CGP::Vagrent::Data::Annotation::getDeletionAnnotationType(), |
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subtype => $subtype); |
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if(defined($tmpGroupClassesHash->{$self->getExonClass}) && defined($tmpGroupClassesHash->{$self->getEssentialSpliceSiteClass})){ |
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# special case, variation spans over the end of the exon. This is a complex change in the transcript |
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push(@classes,$self->getComplexChangeVariantClass); |
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unless($tran->isProteinCoding){ |
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push(@classes,$self->getNonCodingTranscriptVariantClass); |
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} |
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} else { |
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100
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if(defined($tmpGroupClassesHash->{$self->getSpliceRegionClass})){ |
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push(@classes,$self->getSpliceRegionVariantClass); |
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} |
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if(defined($tmpGroupClassesHash->{$self->getEssentialSpliceSiteClass})){ |
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push(@classes,$self->getEssentialSpliceSiteVariantClass); |
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} |
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if(defined($tmpGroupClassesHash->{$self->getIntronClass})){ |
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push(@classes,$self->getIntronVariantClass); |
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} |
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100
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if(defined($tmpGroupClassesHash->{$self->getExonClass})){ |
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if($tran->isProteinCoding){ |
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if($self->_arrayHasString($self->getCDSClass,@groupClasses)){ |
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if($self->_arrayHasString($self->get2KBUpStreamVariantClass,@classes) || $self->_arrayHasString($self->get5PrimeUtrClass,@groupClasses) || $self->_arrayHasString($self->get3PrimeUtrClass,@groupClasses) || $self->_arrayHasString($self->get500BPDownStreamVariantClass,@classes)){ |
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# it overhangs the CDS-to-UTR/upstream/downstream boundry |
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push(@classes,$self->getComplexChangeVariantClass); |
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} else { |
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100
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if(length($wt) % 3 == 0){ |
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push(@classes,$self->getInFrameVariantClass); |
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} else { |
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push(@classes,$self->getFrameShiftVariantClass); |
279
|
|
|
|
} |
280
|
|
|
|
} |
281
|
|
|
|
} |
282
|
|
|
|
} else { |
283
|
|
|
|
push(@classes,$self->getNonCodingTranscriptVariantClass); |
284
|
|
|
|
} |
285
|
|
|
|
} |
286
|
|
|
|
} |
287
|
|
|
|
|
288
|
|
|
|
$anno->addClassification(@classes); |
289
|
|
|
|
|
290
|
|
|
|
return ($anno,@groupClasses); |
291
|
|
|
|
} |
292
|
|
|
|
|
293
|
|
|
|
sub _upstreamVariantCheck { |
294
|
|
505
|
|
my ($self,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset,$classes) = @_; |
295
|
|
|
|
|
296
|
|
|
|
my $upStartScore = 0; |
297
|
|
|
|
my $upEndScore = 0; |
298
|
100
|
|
|
if($mrnaMin > 0 || ($mrnaMin == 0 && $mrnaMinOffset >= 0)){ |
|
50
|
|
|
|
299
|
|
|
|
$upStartScore = 3; |
300
|
|
|
|
} elsif($mrnaMin == 0 && $mrnaMinOffset < 0){ |
301
|
100
|
|
|
if($self->_isWithin2KBUpstreamOffsetDistance($mrnaMinOffset)){ |
|
100
|
|
|
|
302
|
|
|
|
$upStartScore = 2; |
303
|
|
|
|
} elsif($self->_isWithin5KBOffsetDistance($mrnaMinOffset)){ |
304
|
|
|
|
$upStartScore = 1; |
305
|
|
|
|
} |
306
|
|
|
|
} |
307
|
100
|
|
|
if($mrnaMax > 0 || ($mrnaMax == 0 && $mrnaMaxOffset >= 0)){ |
|
50
|
|
|
|
308
|
|
|
|
$upEndScore = 3; |
309
|
|
|
|
} elsif ($mrnaMax == 0 && $mrnaMaxOffset < 0){ |
310
|
100
|
|
|
if($self->_isWithin2KBUpstreamOffsetDistance($mrnaMaxOffset)){ |
|
100
|
|
|
|
311
|
|
|
|
$upEndScore = 2; |
312
|
|
|
|
} elsif($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)){ |
313
|
|
|
|
$upEndScore = 1; |
314
|
|
|
|
} |
315
|
|
|
|
} |
316
|
50
|
|
|
print "up scores: $upStartScore - $upEndScore\n" if($self->_debug); |
317
|
100
|
|
|
if($upStartScore == 0 && $upEndScore == 0){ |
318
|
|
|
|
my $msg = "variant isnt close enough to this transcript, nothing to do"; |
319
|
|
|
|
$self->addMessage($msg); |
320
|
|
|
|
$log->error($msg); |
321
|
|
|
|
return undef; |
322
|
|
|
|
} |
323
|
|
|
|
for(my $i = $upStartScore; $i <= $upEndScore ; $i++){ |
324
|
100
|
|
|
if($i == 1){ |
|
100
|
|
|
|
325
|
|
|
|
push(@$classes,$self->get5KBUpStreamVariantClass); |
326
|
|
|
|
} elsif($i == 2){ |
327
|
|
|
|
push(@$classes,$self->get2KBUpStreamVariantClass); |
328
|
|
|
|
} |
329
|
|
|
|
} |
330
|
100
|
|
|
if($upEndScore < 3){ |
331
|
|
|
|
return 1 |
332
|
|
|
|
} |
333
|
|
|
|
return 0; |
334
|
|
|
|
} |
335
|
|
|
|
|
336
|
|
|
|
sub _downstreamVariantCheck { |
337
|
|
455
|
|
my ($self,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset,$classes) = @_; |
338
|
|
|
|
|
339
|
|
|
|
my $downStartScore = 0; |
340
|
|
|
|
my $downEndScore = 0; |
341
|
100
|
|
|
if($mrnaMin > 0 || ($mrnaMin == 0 && $mrnaMinOffset <= 0)){ |
|
50
|
|
|
|
342
|
|
|
|
$downStartScore = 3; |
343
|
|
|
|
} elsif($mrnaMin == 0 && $mrnaMinOffset > 0){ |
344
|
100
|
|
|
if($self->_isWithin500BPDownstreamOffsetDistance($mrnaMinOffset)){ |
|
100
|
|
|
|
345
|
|
|
|
$downStartScore = 2; |
346
|
|
|
|
} elsif($self->_isWithin5KBOffsetDistance($mrnaMinOffset)){ |
347
|
|
|
|
$downStartScore = 1; |
348
|
|
|
|
} |
349
|
|
|
|
} |
350
|
100
|
|
|
if($mrnaMax > 0 || ($mrnaMax == 0 && $mrnaMaxOffset <= 0)){ |
|
50
|
|
|
|
351
|
|
|
|
$downEndScore = 3; |
352
|
|
|
|
} elsif ($mrnaMax == 0 && $mrnaMaxOffset > 0){ |
353
|
100
|
|
|
if($self->_isWithin500BPDownstreamOffsetDistance($mrnaMaxOffset)){ |
|
100
|
|
|
|
354
|
|
|
|
$downEndScore = 2; |
355
|
|
|
|
} elsif($self->_isWithin5KBOffsetDistance($mrnaMaxOffset)){ |
356
|
|
|
|
$downEndScore = 1; |
357
|
|
|
|
} |
358
|
|
|
|
} |
359
|
50
|
|
|
print "down scores: $downStartScore - $downEndScore\n" if($self->_debug); |
360
|
100
|
|
|
if($downStartScore == 0 && $downEndScore == 0){ |
361
|
|
|
|
my $msg = "variant isnt close enough to this transcript, nothing to do"; |
362
|
|
|
|
$self->addMessage($msg); |
363
|
|
|
|
$log->error($msg); |
364
|
|
|
|
return undef; |
365
|
|
|
|
} |
366
|
|
|
|
for(my $i = $downEndScore ; $i <= $downStartScore; $i++){ |
367
|
100
|
|
|
if($i == 1){ |
|
100
|
|
|
|
368
|
|
|
|
push(@$classes,$self->get5KBDownStreamVariantClass); |
369
|
|
|
|
} elsif($i == 2){ |
370
|
|
|
|
push(@$classes,$self->get500BPDownStreamVariantClass); |
371
|
|
|
|
} |
372
|
|
|
|
} |
373
|
100
|
|
|
if($downStartScore < 3){ |
374
|
|
|
|
return 1; |
375
|
|
|
|
} |
376
|
|
|
|
return 0; |
377
|
|
|
|
} |
378
|
|
|
|
|
379
|
|
|
|
sub _classifyDeletion { |
380
|
|
413
|
|
my ($self,$tran,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset) = @_; |
381
|
|
|
|
# big scary logic ladder time |
382
|
|
|
|
my $grpCls; |
383
|
|
|
|
my @exons = $tran->getExons; |
384
|
|
|
|
@exons = sort {$a->getRnaMinPos <=> $b->getRnaMinPos} @exons; |
385
|
50
|
|
|
print "$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset\n" if($self->_debug); |
386
|
|
|
|
for(my $i = 0 ; $i < scalar(@exons) ; $i++){ |
387
|
|
|
|
my $e = $exons[$i]; |
388
|
100
|
|
|
if($mrnaMin > $e->getRnaMaxPos){ |
389
|
|
|
|
# exon occurs before mutation in transcript, ignore |
390
|
|
|
|
next; |
391
|
|
|
|
} |
392
|
100
|
|
|
if($mrnaMax < $e->getRnaMinPos){ |
393
|
|
|
|
# exon occurs after mutation in transcript, ignore |
394
|
|
|
|
next; |
395
|
|
|
|
} |
396
|
|
|
|
# if we get here the variant is somehow linked to the current exon |
397
|
|
|
|
|
398
|
|
|
|
# check to see if the variant overlaps the exon |
399
|
100
|
|
|
if(($mrnaMin < $e->getRnaMaxPos || ($mrnaMin == $e->getRnaMaxPos && $mrnaMinOffset == 0)) && ($mrnaMax > $e->getRnaMinPos || ($mrnaMax == $e->getRnaMinPos && $mrnaMaxOffset == 0))){ |
400
|
|
|
|
$grpCls->{$self->getExonClass}++; |
401
|
|
|
|
} |
402
|
50
|
|
|
print Dumper($e) if($self->_debug); |
403
|
|
|
|
# check to see if the variant effects the area before the exon |
404
|
100
|
|
|
if($mrnaMin < $e->getRnaMinPos || ($mrnaMin == $e->getRnaMinPos && $mrnaMinOffset < 0)){ |
405
|
|
|
|
# variant starts before the exon |
406
|
100
|
|
|
if($mrnaMin < $e->getRnaMinPos || $self->_isIntronicOffsetDistance($mrnaMinOffset)){ |
|
100
|
|
|
|
407
|
|
|
|
# variant starts in the intron |
408
|
100
|
|
|
if($mrnaMax > $e->getRnaMinPos || ($mrnaMax == $e->getRnaMinPos && $mrnaMaxOffset == 0)){ |
|
100
|
|
|
|
|
50
|
|
|
|
409
|
|
|
|
# variant ends after or on the start of the exon, so it gets all 3 terms |
410
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
411
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
412
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
413
|
|
|
|
} elsif($self->_isIntronicOffsetDistance($mrnaMaxOffset)){ |
414
|
|
|
|
# variant also ends in the intron |
415
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
416
|
|
|
|
} elsif($mrnaMaxOffset < 0 && $mrnaMaxOffset >= $self->_getConsesnsusSpliceBeforeBoundry){ |
417
|
|
|
|
# variant ends in the essential splice site |
418
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
419
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
420
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
421
|
|
|
|
} else { |
422
|
|
|
|
# variant ends in the splice region |
423
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
424
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
425
|
|
|
|
} |
426
|
|
|
|
} elsif ($mrnaMin == $e->getRnaMinPos && $mrnaMinOffset >= $self->_getConsesnsusSpliceBeforeBoundry){ |
427
|
|
|
|
# variant starts in the essential splice site |
428
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
429
|
|
|
|
} else { |
430
|
|
|
|
# variant starts in the splice region |
431
|
100
|
|
|
if($mrnaMax > $e->getRnaMinPos || ($mrnaMax == $e->getRnaMinPos && $mrnaMaxOffset == 0)){ |
|
100
|
|
|
|
432
|
|
|
|
# variant ends after the start of the exon, so |
433
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
434
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
435
|
|
|
|
} elsif($mrnaMaxOffset < 0 && $mrnaMaxOffset >= $self->_getConsesnsusSpliceBeforeBoundry){ |
436
|
|
|
|
# variant ends in the essential splice site |
437
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
438
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
439
|
|
|
|
} else { |
440
|
|
|
|
# variant also ends in the splice region |
441
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
442
|
|
|
|
} |
443
|
|
|
|
} |
444
|
|
|
|
} |
445
|
|
|
|
|
446
|
|
|
|
# check to see if the variant effects the area after the exon |
447
|
100
|
|
|
if($mrnaMax > $e->getRnaMaxPos || ($mrnaMax == $e->getRnaMaxPos && $mrnaMaxOffset > 0)){ |
448
|
|
|
|
# variant ends after the exon |
449
|
100
|
|
|
if($mrnaMax > $e->getRnaMaxPos || $self->_isIntronicOffsetDistance($mrnaMaxOffset)){ |
|
100
|
|
|
|
450
|
|
|
|
# variant ends in the intron |
451
|
100
|
|
|
if($mrnaMin < $e->getRnaMaxPos || ($mrnaMin == $e->getRnaMaxPos && $mrnaMinOffset == 0)){ |
|
100
|
|
|
|
|
100
|
|
|
|
452
|
|
|
|
# variant starts before or on the end of the exon, so it gets all 3 terms |
453
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
454
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
455
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
456
|
|
|
|
} elsif($self->_isIntronicOffsetDistance($mrnaMinOffset)){ |
457
|
|
|
|
# variant also starts in the intron |
458
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
459
|
|
|
|
} elsif ($mrnaMinOffset > 0 && $mrnaMinOffset <= $self->_getConsesnsusSpliceAfterBoundry){ |
460
|
|
|
|
# variant starts in the essential splice site |
461
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
462
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
463
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
464
|
|
|
|
} else { |
465
|
|
|
|
# variant must start in the splice region |
466
|
|
|
|
$grpCls->{$self->getIntronClass}++; |
467
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
468
|
|
|
|
} |
469
|
|
|
|
} elsif($mrnaMax == $e->getRnaMaxPos && $mrnaMaxOffset <= $self->_getConsesnsusSpliceAfterBoundry){ |
470
|
|
|
|
# variant ends in the essential splice site |
471
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
472
|
|
|
|
} else { |
473
|
|
|
|
# variant ends in the splice region |
474
|
100
|
|
|
if($mrnaMin < $e->getRnaMaxPos || ($mrnaMin == $e->getRnaMaxPos && $mrnaMinOffset == 0)){ |
|
100
|
|
|
|
475
|
|
|
|
# variant starts before or on the end of the exon, so it gets all 3 terms |
476
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
477
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
478
|
|
|
|
} elsif ($mrnaMinOffset > 0 && $mrnaMinOffset <= $self->_getConsesnsusSpliceAfterBoundry){ |
479
|
|
|
|
# variant starts in the essential splice site |
480
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
481
|
|
|
|
$grpCls->{$self->getEssentialSpliceSiteClass}++; |
482
|
|
|
|
} else { |
483
|
|
|
|
# variant must start in the splice region |
484
|
|
|
|
$grpCls->{$self->getSpliceRegionClass}++; |
485
|
|
|
|
} |
486
|
|
|
|
} |
487
|
|
|
|
} |
488
|
|
|
|
} |
489
|
50
|
|
|
print Dumper($grpCls) if($self->_debug); |
490
|
|
|
|
return $grpCls; |
491
|
|
|
|
} |
492
|
|
|
|
|
493
|
|
|
|
sub _getCDSDescriptionString { |
494
|
|
86
|
|
my ($self,$tran,$mutStart,$mutEnd,$mutStartOffset,$mutEndOffset,$wt,$mt) = @_; |
495
|
|
|
|
my $desc = undef; |
496
|
100
|
|
|
if($mutStart == 1 && $mutEnd == length($tran->getCdsSeq)){ |
497
|
|
|
|
$desc = 'c.0'; |
498
|
|
|
|
} else { |
499
|
|
|
|
$desc = $self->_generateDNADelDescriptionString('c.',$mutStart,$mutEnd,$mutStartOffset,$mutEndOffset,$wt); |
500
|
|
|
|
} |
501
|
|
|
|
return $desc; |
502
|
|
|
|
} |
503
|
|
|
|
|
504
|
|
|
|
sub _generateDNADelDescriptionString { |
505
|
|
260
|
|
my ($self,$pre,$mutStart,$mutEnd,$mutStartOffset,$mutEndOffset,$wt) = @_; |
506
|
|
|
|
my $desc = 'WIBBLE'; |
507
|
100
|
|
|
if($mutStart == $mutEnd && $mutStartOffset == $mutEndOffset){ |
508
|
|
|
|
# single base change |
509
|
100
|
|
|
if($mutStartOffset > 0){ |
|
100
|
|
|
|
|
50
|
|
|
|
510
|
|
|
|
$desc = $pre.$mutStart.'+'.$mutStartOffset.'del'.$wt; |
511
|
|
|
|
} elsif($mutStartOffset < 0){ |
512
|
|
|
|
$desc = $pre.$mutStart.$mutStartOffset.'del'.$wt; |
513
|
|
|
|
} elsif ($mutStartOffset == 0) { |
514
|
|
|
|
$desc = $pre.$mutStart.'del'.$wt; |
515
|
|
|
|
} |
516
|
|
|
|
} else { |
517
|
|
|
|
# multi base change |
518
|
100
|
|
|
if($mutStartOffset > 0){ |
|
100
|
|
|
|
|
50
|
|
|
|
519
|
|
|
|
$desc = $pre.$mutStart.'+'.$mutStartOffset.'_'; |
520
|
|
|
|
} elsif($mutStartOffset < 0){ |
521
|
|
|
|
$desc = $pre.$mutStart.$mutStartOffset.'_'; |
522
|
|
|
|
} elsif($mutStartOffset == 0) { |
523
|
|
|
|
$desc = $pre.$mutStart.'_'; |
524
|
|
|
|
} |
525
|
|
|
|
|
526
|
100
|
|
|
if($mutEndOffset > 0){ |
|
100
|
|
|
|
|
50
|
|
|
|
527
|
|
|
|
$desc .= $mutEnd.'+'.$mutEndOffset.'del'; |
528
|
|
|
|
} elsif($mutEndOffset < 0){ |
529
|
|
|
|
$desc .= $mutEnd.$mutEndOffset.'del'; |
530
|
|
|
|
} elsif($mutEndOffset == 0){ |
531
|
|
|
|
$desc .= $mutEnd.'del'; |
532
|
|
|
|
} |
533
|
|
|
|
|
534
|
100
|
|
|
if(length($wt) > 15){ |
535
|
|
|
|
$desc .= length($wt); |
536
|
|
|
|
} else { |
537
|
|
|
|
$desc .= $wt; |
538
|
|
|
|
} |
539
|
|
|
|
} |
540
|
|
|
|
return $desc; |
541
|
|
|
|
} |
542
|
|
|
|
|
543
|
|
|
|
sub _getWildTypeStringForRNAAnno { |
544
|
|
444
|
|
my ($self,$var,$tran) = @_; |
545
|
|
|
|
my $wt = ''; |
546
|
|
|
|
my @seq = split('',$var->getDeletedSequence); |
547
|
|
|
|
my @exons = sort{$a->getMinPos <=> $b->getMinPos} $tran->getExons; |
548
|
|
|
|
for(my $i = $var->getMinPos, my $c = 0; $c < scalar(@seq); $i++, $c++){ |
549
|
|
|
|
my $isExonic = 0; |
550
|
|
|
|
my $ec = 0; |
551
|
|
|
|
my $use = 0; |
552
|
|
|
|
foreach my $e(@exons){ |
553
|
|
|
|
$ec++; |
554
|
100
|
|
|
if($i > $e->getMaxPos){ # base after exon, continue |
|
100
|
|
|
|
|
50
|
|
|
|
555
|
100
|
|
|
if($ec == scalar(@exons)){ # if the base is after the last exon we don't want to use it |
556
|
|
|
|
$use = 0; |
557
|
|
|
|
} else { |
558
|
|
|
|
$use = 1; |
559
|
|
|
|
} |
560
|
|
|
|
next; |
561
|
|
|
|
} elsif($i >= $e->getMinPos && $i <= $e->getMaxPos){ # base in exon, quit |
562
|
|
|
|
$isExonic = 1; |
563
|
|
|
|
$use = 1; |
564
|
|
|
|
last; |
565
|
|
|
|
} elsif($i < $e->getMinPos){ # base before exon, quit |
566
|
100
|
|
|
$use = 1 unless($ec==1); # ignore the base if its before the first exon |
567
|
|
|
|
last; |
568
|
|
|
|
} |
569
|
|
|
|
} |
570
|
100
|
|
|
next unless($use == 1); # skip the base if its not flagged for use |
571
|
100
|
|
|
if($isExonic){ |
572
|
|
|
|
$wt .= uc($seq[$c]); |
573
|
|
|
|
} else { |
574
|
|
|
|
$wt .= lc($seq[$c]); |
575
|
|
|
|
} |
576
|
|
|
|
} |
577
|
100
|
|
|
if($tran->getStrand == -1){ |
578
|
|
|
|
$wt = $self->_revcompSeq($wt); |
579
|
|
|
|
} |
580
|
|
|
|
return $wt; |
581
|
|
|
|
} |
582
|
|
|
|
|
583
|
|
|
|
sub _getWildTypeStringForCDSAnno { |
584
|
|
165
|
|
my ($self,$var,$tran,$rAnnot) = @_; |
585
|
|
|
|
my $wt = ''; |
586
|
100
|
|
|
if($rAnnot->hasClassification($self->getInFrameVariantClass) || $rAnnot->hasClassification($self->getFrameShiftVariantClass)){ |
|
100
|
|
|
|
587
|
|
|
|
my @seq = split('',$var->getDeletedSequence); |
588
|
|
|
|
my @exons = sort{$a->getMinPos <=> $b->getMinPos} $tran->getExons; |
589
|
|
|
|
for(my $i = $var->getMinPos, my $c = 0; $c < scalar(@seq); $i++, $c++){ |
590
|
|
|
|
my $isCod = 0; |
591
|
|
|
|
foreach my $e(@exons){ |
592
|
100
|
|
|
next unless($i >= $e->getMinPos && $i <= $e->getMaxPos); # base is in this exon |
593
|
100
|
|
|
if($tran->getStrand == 1){ |
594
|
|
|
|
my $pos = ($i - $e->getMinPos) + $e->getRnaMinPos; |
595
|
50
|
|
|
if($pos >= $tran->getCdsMinPos && $pos <= $tran->getCdsMaxPos){ |
596
|
|
|
|
$isCod = 1; |
597
|
|
|
|
last; |
598
|
|
|
|
} |
599
|
|
|
|
} else { |
600
|
|
|
|
my $pos = $e->getRnaMaxPos - ($i - $e->getMinPos); |
601
|
50
|
|
|
if($pos >= $tran->getCdsMinPos && $pos <= $tran->getCdsMaxPos){ |
602
|
|
|
|
$isCod = 1; |
603
|
|
|
|
last; |
604
|
|
|
|
} |
605
|
|
|
|
} |
606
|
|
|
|
} |
607
|
50
|
|
|
if($isCod){ |
608
|
|
|
|
$wt .= uc($seq[$c]); |
609
|
|
|
|
} |
610
|
|
|
|
} |
611
|
100
|
|
|
if($tran->getStrand == -1){ |
612
|
|
|
|
$wt = $self->_revcompSeq($wt); |
613
|
|
|
|
} |
614
|
|
|
|
} elsif ($rAnnot->hasClassification($self->getComplexChangeVariantClass)){ |
615
|
100
|
|
|
if($rAnnot->getMinPos <= $tran->getCdsMinPos || $rAnnot->getMaxPos >= $tran->getCdsMaxPos){ |
616
|
|
|
|
# variant exists outside the CDS, have to truncate it back |
617
|
|
|
|
my $len = ($tran->getCdsMaxPos - $tran->getCdsMinPos) + 1; |
618
|
|
|
|
my ($genomicCdsLow,$genomicCdsHigh) = $self->_calculateGenomicCdsPosition($tran); |
619
|
|
|
|
my $newDelMin = undef; |
620
|
|
|
|
my $newDelMax = undef; |
621
|
|
|
|
my $newDelSeq = $var->getDeletedSequence; |
622
|
100
|
|
|
if($var->getMinPos < $genomicCdsLow){ |
623
|
|
|
|
$newDelMin = $genomicCdsLow; |
624
|
|
|
|
substr($newDelSeq,0,($newDelMin - $var->getMinPos),''); |
625
|
|
|
|
} else { |
626
|
|
|
|
$newDelMin = $var->getMinPos; |
627
|
|
|
|
} |
628
|
100
|
|
|
if($var->getMaxPos > $genomicCdsHigh){ |
629
|
|
|
|
$newDelMax = $genomicCdsHigh; |
630
|
|
|
|
$newDelSeq = substr($newDelSeq,0,($newDelMax - $newDelMin) + 1); |
631
|
|
|
|
} else { |
632
|
|
|
|
$newDelMax = $var->getMaxPos; |
633
|
|
|
|
} |
634
|
|
|
|
|
635
|
|
|
|
my $newDel = Sanger::CGP::Vagrent::Data::Deletion->new( |
636
|
|
|
|
'species' => $var->getSpecies, |
637
|
|
|
|
'genomeVersion' => $var->getGenomeVersion, |
638
|
|
|
|
'chr' => $var->getChr, |
639
|
|
|
|
'minpos' => $newDelMin, |
640
|
|
|
|
'maxpos' => $newDelMax, |
641
|
|
|
|
'delseq' => $newDelSeq); |
642
|
|
|
|
|
643
|
|
|
|
$wt = $self->_getWildTypeStringForRNAAnno($newDel,$tran); |
644
|
|
|
|
} else { |
645
|
|
|
|
$wt = $self->_getWildTypeStringForRNAAnno($var,$tran); |
646
|
|
|
|
} |
647
|
|
|
|
} else { |
648
|
|
|
|
$wt = $self->_getWildTypeStringForRNAAnno($var,$tran); |
649
|
|
|
|
} |
650
|
|
|
|
$wt =~ s/u/t/ig; |
651
|
|
|
|
return $wt; |
652
|
|
|
|
} |
653
|
|
|
|
|
654
|
|
|
|
sub _getMutantStringForCDSAnno { |
655
|
|
86
|
|
my ($self,$var,$tran,$rAnnot) = @_; |
656
|
|
|
|
return '-'; |
657
|
|
|
|
} |
658
|
|
|
|
|
659
|
|
|
|
sub _getMutatedCdsSequence { |
660
|
|
18
|
|
my ($self,$wtDna,$min,$max,$mt) = @_; |
661
|
|
|
|
my $codingDelLength = ($max - $min) + 1; |
662
|
|
|
|
my $mtDna = $wtDna; |
663
|
|
|
|
substr($mtDna,($min - 1),$codingDelLength,''); |
664
|
|
|
|
return $mtDna |
665
|
|
|
|
} |
666
|
|
|
|
|
667
|
|
|
|
sub _getCdsMinPosForProteinCalculation { |
668
|
|
36
|
|
my ($self,$cAnnot) = @_; |
669
|
|
|
|
my $min = undef; |
670
|
50
|
|
|
if($cAnnot->getMinOffset > 0){ |
671
|
|
|
|
$min = $cAnnot->getMinPos + 1; |
672
|
|
|
|
} else { |
673
|
|
|
|
$min = $cAnnot->getMinPos; |
674
|
|
|
|
} |
675
|
|
|
|
return $min; |
676
|
|
|
|
} |
677
|
|
|
|
|
678
|
|
|
|
sub _getCdsMaxPosForProteinCalculation { |
679
|
|
36
|
|
my ($self,$cAnnot) = @_; |
680
|
|
|
|
my $max = undef; |
681
|
50
|
|
|
if($cAnnot->getMaxOffset < 0){ |
682
|
|
|
|
$max = $cAnnot->getMaxPos - 1; |
683
|
|
|
|
} else { |
684
|
|
|
|
$max = $cAnnot->getMaxPos; |
685
|
|
|
|
} |
686
|
|
|
|
return $max; |
687
|
|
|
|
} |
688
|
|
|
|
|
689
|
|
|
|
sub _safetyCheck { |
690
|
|
505
|
|
my ($self,$var,$tran,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset) = @_; |
691
|
|
|
|
my $tranString = $self->_getTranscriptSubstringForCheck($tran,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset); |
692
|
50
|
|
|
unless(defined($tranString)){ |
693
|
|
|
|
return 0; |
694
|
|
|
|
} |
695
|
|
|
|
my $genoString = $self->_getExonicGenomicSubstringForCheck($var,$tran); |
696
|
50
|
|
|
unless(defined($genoString)){ |
697
|
|
|
|
return 0; |
698
|
|
|
|
} |
699
|
50
|
|
|
if($self->_debug){ |
700
|
|
|
|
print 'DELSEQ = '.$var->getDeletedSequence."\n"; |
701
|
|
|
|
print 'TRANSEQ = '.$tranString."\n"; |
702
|
|
|
|
print 'GENOSEQ = '.$genoString."\n"; |
703
|
|
|
|
} |
704
|
100
|
|
|
if(length($tranString) == 0 && length($genoString) == 0){ |
|
50
|
|
|
|
705
|
|
|
|
# not exonic sequence, no transcript sequence to check, just have to hope its OK |
706
|
|
|
|
return 1; |
707
|
|
|
|
} elsif(uc($tranString) eq uc($genoString)){ |
708
|
|
|
|
return 1; |
709
|
|
|
|
} |
710
|
|
|
|
return 0; |
711
|
|
|
|
} |
712
|
|
|
|
|
713
|
|
|
|
sub _getTranscriptSubstringForCheck { |
714
|
|
505
|
|
my ($self,$tran,$mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset) = @_; |
715
|
|
|
|
my $substr = undef; |
716
|
|
|
|
my $pos = undef; |
717
|
|
|
|
my $len = undef; |
718
|
50
|
|
|
print "TRAN SUB STR $mrnaMin,$mrnaMinOffset,$mrnaMax,$mrnaMaxOffset\n" if($self->_debug); |
719
|
100
|
|
|
if($mrnaMin == 0 && $mrnaMinOffset > 0){ |
|
100
|
|
|
|
|
100
|
|
|
|
720
|
|
|
|
# variant starts after transcript, nothing to do |
721
|
|
|
|
return ''; |
722
|
|
|
|
} elsif($mrnaMax == 0 && $mrnaMaxOffset < 0){ |
723
|
|
|
|
# variant ends before transcript, nothing to do |
724
|
|
|
|
return ''; |
725
|
|
|
|
} elsif($mrnaMinOffset == 0 && $mrnaMaxOffset == 0){ |
726
|
|
|
|
$pos = $mrnaMin - 1; |
727
|
|
|
|
$len = ($mrnaMax - $mrnaMin) + 1 |
728
|
|
|
|
} else { |
729
|
|
|
|
my $leftAnchor; |
730
|
|
|
|
my $rightAnchor; |
731
|
100
|
|
|
if($mrnaMinOffset > 0){ |
732
|
|
|
|
$leftAnchor = $mrnaMin + 1; |
733
|
|
|
|
} else { |
734
|
|
|
|
$leftAnchor = $mrnaMin; |
735
|
|
|
|
} |
736
|
100
|
|
|
if($mrnaMaxOffset < 0){ |
737
|
|
|
|
$rightAnchor = $mrnaMax - 1; |
738
|
|
|
|
} else { |
739
|
|
|
|
$rightAnchor = $mrnaMax; |
740
|
|
|
|
} |
741
|
100
|
|
|
$leftAnchor = 1 if $leftAnchor < 1; |
742
|
100
|
|
|
$rightAnchor = length($tran->getcDNASeq) if($rightAnchor == 0); |
743
|
50
|
|
|
print "ANCHOR $leftAnchor $rightAnchor\n" if($self->_debug); |
744
|
100
|
|
|
if($leftAnchor > $rightAnchor){ |
745
|
|
|
|
# its an intronic change that doesn't span any coding bases |
746
|
|
|
|
return ''; |
747
|
|
|
|
} |
748
|
|
|
|
$pos = $leftAnchor - 1; |
749
|
|
|
|
$len = ($rightAnchor - $leftAnchor) + 1; |
750
|
|
|
|
|
751
|
|
|
|
} |
752
|
50
|
|
|
print "FINAL $pos $len\n" if($self->_debug); |
753
|
|
|
|
$substr = substr($tran->getcDNASeq,$pos,$len); |
754
|
|
|
|
return $substr; |
755
|
|
|
|
} |
756
|
|
|
|
|
757
|
|
|
|
sub _getExonicGenomicSubstringForCheck { |
758
|
|
505
|
|
my ($self,$var,$tran) = @_; |
759
|
|
|
|
my $substr = undef; |
760
|
|
|
|
my $c = 0; |
761
|
|
|
|
my $beforeC = 0; |
762
|
|
|
|
my $duringC = 0; |
763
|
|
|
|
foreach my $e ($tran->getExonsGenomicOrder){ |
764
|
|
|
|
$c++; |
765
|
100
|
|
|
if($e->getMaxPos < $var->getMinPos){ |
766
|
|
|
|
# exon before deletion - skip |
767
|
50
|
|
|
print "EXON $c BEFORE\n" if($self->_debug); |
768
|
|
|
|
$beforeC++; |
769
|
|
|
|
next; |
770
|
|
|
|
} |
771
|
100
|
|
|
if($var->getMinPos <= $e->getMaxPos && $e->getMinPos <= $var->getMaxPos){ |
772
|
|
|
|
# overlap |
773
|
|
|
|
$duringC++; |
774
|
|
|
|
my $start = ($e->getMinPos - $var->getMinPos) + 1; |
775
|
|
|
|
my $end = ($e->getMaxPos - $var->getMinPos) + 1; |
776
|
100
|
|
|
$start = 1 if($start < 1); |
777
|
100
|
|
|
$end = length($var->getDeletedSequence) if($end > length($var->getDeletedSequence)); |
778
|
|
|
|
|
779
|
|
|
|
my $pos = $start - 1; |
780
|
|
|
|
my $len = ($end - $start) + 1; |
781
|
|
|
|
my $tmp = substr($var->getDeletedSequence,$pos,$len); |
782
|
100
|
|
|
if(defined($substr)){ |
783
|
|
|
|
$substr .= $tmp; |
784
|
|
|
|
} else { |
785
|
|
|
|
$substr = $tmp; |
786
|
|
|
|
} |
787
|
50
|
|
|
print "EXON $c DURING $start $end $tmp\n" if($self->_debug); |
788
|
|
|
|
} |
789
|
100
|
|
|
if($var->getMaxPos < $e->getMinPos){ |
790
|
50
|
|
|
print "EXON $c AFTER\n" if($self->_debug); |
791
|
|
|
|
# exon after deletion |
792
|
100
|
|
|
if(!defined($substr)){ |
793
|
|
|
|
# its not a coding change; |
794
|
|
|
|
return ''; |
795
|
|
|
|
} |
796
|
|
|
|
} |
797
|
|
|
|
} |
798
|
100
|
|
|
if($duringC == 0){ |
799
|
|
|
|
# variant doesn't overlap any exons |
800
|
|
|
|
return ''; |
801
|
|
|
|
} |
802
|
100
|
|
|
if($tran->getStrand == -1){ |
803
|
|
|
|
$substr = $self->_revcompSeq($substr); |
804
|
|
|
|
} |
805
|
|
|
|
return $substr; |
806
|
|
|
|
} |
807
|
|
|
|
|
808
|
|
|
|
sub _getDefaultCDSAnnotationType { |
809
|
|
86
|
|
return Sanger::CGP::Vagrent::Data::Annotation::getDeletionAnnotationType(); |
810
|
|
|
|
} |
811
|
|
|
|
|
812
|
|
|
|
sub _getDefaultProteinAnnotationType { |
813
|
|
3
|
|
return Sanger::CGP::Vagrent::Data::Annotation::getDeletionAnnotationType(); |
814
|
|
|
|
} |
815
|
|
|
|
|
816
|
|
|
|
|
817
|
|
|
|
=head1 NAME |
818
|
|
|
|
|
819
|
|
|
|
Sanger::CGP::Vagrent::Annotators::DeletionAnnotator - Annotator for deletion variants |
820
|
|
|
|
|
821
|
|
|
|
=head1 DESCRIPTION |
822
|
|
|
|
|
823
|
|
|
|
This annotates deletion variants, it provides L<AnnotatonGroups|Sanger::CGP::Vagrent::Data::AnnotationGroup> for each transcript returned from the L<TranscriptSource|Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource> |
824
|
|
|
|
|
825
|
|
|
|
It will only process L<Sanger::CGP::Vagrent::Data::Deletion|Sanger::CGP::Vagrent::Data::Deletion> objects, if any other L<Variation|Sanger::CGP::Vagrent::Data::AbstractVariation> objects are sent in it will return an empty answer. |
826
|
|
|
|
|
827
|
|
|
|
It inherits from L<Sanger::CGP::Vagrent::Annotators::AbstractAnnotator|Sanger::CGP::Vagrent::Annotators::AbstractAnnotator>. |
828
|
|
|
|
|
829
|
|
|
|
=head1 METHODS |
830
|
|
|
|
|
831
|
|
|
|
See L<Sanger::CGP::Vagrent::Annotators::AbstractAnnotator|Sanger::CGP::Vagrent::Annotators::AbstractAnnotator> |