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package Sanger::CGP::Vagrent::TranscriptSource::FileBasedTranscriptSource; |
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##########LICENCE########## |
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# Copyright (c) 2014 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 Carp; |
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use Log::Log4perl; |
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use Data::Dumper; |
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use Const::Fast qw(const); |
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use Bio::DB::HTS; |
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use Bio::DB::HTS::Tabix; |
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use Sanger::CGP::Vagrent::Data::Transcript; |
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use Sanger::CGP::Vagrent::Data::Exon; |
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use Sanger::CGP::Vagrent qw($VERSION); |
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use base qw(Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource); |
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my $log = Log::Log4perl->get_logger(__PACKAGE__); |
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const my $SEARCH_BUFFER => 10000; |
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const my $GENE_GRAB_TEMPLATE => 'tabix %s %s | cut -s -f5 | uniq |'; |
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const my $TRANSCRIPT_GRAB_TEMPLATE => q{tabix %s %s | awk '$5 == "%s" { print $0;}' | cut -s -f7 |}; |
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1; |
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sub getTranscripts { |
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my ($self,$gp) = @_; |
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unless(defined($gp) && $gp->isa('Sanger::CGP::Vagrent::Data::AbstractGenomicPosition')){ |
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$log->error("Did not recieve a Sanger::CGP::Vagrent::Data::AbstractGenomicPosition object"); |
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return undef; |
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} |
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my $trans = $self->_getTranscriptsFromCache($gp); |
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return @$trans if defined $trans; |
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return; |
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} |
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sub getTranscriptsForNextGeneInDumpRegion { |
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my ($self) = @_; |
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my $gr = $self->getDumpRegion; |
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$log->logcroak('must define a dump region before trying to loop over the genes') unless defined $gr; |
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if($gr->getMinPos == $gr->getMaxPos && $gr->getMaxPos == 0){ |
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# full sequence region scan |
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$self->{_dumpInfo}->{_fullSeq} = 1; |
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} else { |
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$self->{_dumpInfo}->{_fullSeq} = 0; |
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} |
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$self->_populateGeneList($gr) unless defined $self->{_dumpInfo}->{_geneList}; |
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$self->_getDumpTranscriptStore($gr) unless defined $self->{_dumpInfo}->{_transcriptStore}; |
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my $geneListSize = scalar @{$self->{_dumpInfo}->{_geneList}}; |
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for(my $i = $self->{_dumpInfo}->{_counter} ; $i <= $geneListSize ; $i++){ |
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$self->{_dumpInfo}->{_counter}++; |
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next unless(defined $self->{_dumpInfo}->{_geneList}->[$i]); |
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my $transList = $self->_getTranascriptsForGeneName($gr,$self->{_dumpInfo}->{_geneList}->[$i]); |
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next unless(defined $transList && scalar(@$transList) > 0); |
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return @$transList; |
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} |
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return undef; |
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} |
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sub _getTranascriptsForGeneName { |
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my ($self,$gr,$genename) = @_; |
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my $out; |
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my $cmd = sprintf $TRANSCRIPT_GRAB_TEMPLATE, $self->{_cache}, $self->_generateLocationString($gr), $genename; |
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open my $fh, $cmd or $log->logcroak("unable to run transcript lookup for gene name $genename: $cmd"); |
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while(<$fh>){ |
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my $VAR1; |
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eval $_; |
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push(@$out,$VAR1); |
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} |
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close $fh; |
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return $out; |
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} |
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sub _getDumpTranscriptStore { |
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my ($self,$gr) = @_; |
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} |
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sub _populateGeneList { |
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my ($self,$gr) = @_; |
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my $cmd = sprintf $GENE_GRAB_TEMPLATE, $self->{_cache}, $self->_generateLocationString($gr); |
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open my $fh, $cmd or $log->logcroak('unable to run gene name lookup for region dump'); |
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@{$self->{_dumpInfo}->{_geneList}} = <$fh>; |
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close $fh; |
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chomp @{$self->{_dumpInfo}->{_geneList}}; |
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$self->{_dumpInfo}->{_counter} = 0; |
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} |
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sub _generateLocationString { |
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my ($self,$gr) = @_; |
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return $gr->getChr.':'.$gr->getMinPos.'-'.$gr->getMaxPos; |
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} |
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sub _getTranscriptsFromCache { |
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my ($self,$gp) = @_; |
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$self->{_cache_tbx} = Bio::DB::HTS::Tabix->new(filename => $self->{_cache}) unless defined $self->{_cache_tbx}; |
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my $min; |
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my $max = $gp->getMaxPos + $SEARCH_BUFFER; |
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if($gp->getMinPos() < $SEARCH_BUFFER){ |
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$min = 0; |
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} else { |
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$min = ($gp->getMinPos - $SEARCH_BUFFER); |
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} |
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my $iter = $self->{_cache_tbx}->query(sprintf '%s:%d-%d', $gp->getChr(),$min,$max); |
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return undef unless defined $iter; |
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my $out = undef; |
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while(my $ret = $iter->next){ |
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my $raw = (split("\t",$ret))[6]; |
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my $VAR1; |
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eval $raw; |
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$VAR1->{_cdnaseq} = $self->_getTranscriptSeq($VAR1); |
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push @$out, $VAR1; |
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} |
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return $out; |
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} |
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sub _init { |
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my $self = shift; |
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my %vars = @_; |
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foreach my $k(keys(%vars)){ |
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if($k eq 'cache'){ |
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$self->_setCacheFile($vars{$k}); |
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} |
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} |
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} |
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sub _setCacheFile { |
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my ($self,$cache) = @_; |
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unless(-e $cache && -f $cache && -r $cache){ |
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$log->logcroak("Specified cache file is unreadable: $cache"); |
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} |
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my $cache_index = $cache .".tbi"; |
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unless(-e $cache_index && -f $cache_index && -r $cache_index){ |
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$log->logcroak("cache index file is unreadable: $cache_index"); |
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} |
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my $fa = $cache; |
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$fa =~ s/\.cache.+$/.fa/; |
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unless(-e $fa && -f $fa && -r $fa){ |
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$log->logcroak("cache fasta file is unreadable: $fa"); |
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} |
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my $fai = $fa . ".fai"; |
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unless(-e $fai && -f $fai && -r $fai){ |
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$log->logcroak("cache fasta index file is unreadable: $fai"); |
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} |
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$self->{_cache} = $cache; |
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$self->{_cache_fa} = $fa; |
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} |
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sub _getTranscriptSeq { |
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my ($self,$trans) = @_; |
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unless(defined $self->{_fai_obj}){ |
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$self->{_fai_obj} = Bio::DB::HTS::Fai->load($self->{_cache_fa}); |
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} |
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return $self->{_fai_obj}->fetch($trans->getAccession); |
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} |