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package Sanger::CGP::Vcf::VcfUtil; |
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##########LICENCE########## |
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# Copyright (c) 2014,2015 Genome Research Ltd. |
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# |
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# Author: Jon Hinton <cgpit@sanger.ac.uk> |
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# |
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# This file is part of cgpVcf. |
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# |
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# cgpVcf 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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# |
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# 1. The usage of a range of years within a copyright statement contained within |
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# this distribution should be interpreted as being equivalent to a list of years |
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# including the first and last year specified and all consecutive years between |
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# them. For example, a copyright statement that reads âCopyright (c) 2005, 2007- |
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# 2009, 2011-2012â should be interpreted as being identical to a statement that |
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# reads âCopyright (c) 2005, 2007, 2008, 2009, 2011, 2012â and a copyright |
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# statement that reads âCopyright (c) 2005-2012â should be interpreted as being |
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# identical to a statement that reads âCopyright (c) 2005, 2006, 2007, 2008, |
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# 2009, 2010, 2011, 2012â." |
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########## LICENCE ########## |
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use Sanger::CGP::Vcf; |
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our $VERSION = Sanger::CGP::Vcf->VERSION; |
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use strict; |
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use warnings FATAL => 'all'; |
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use Carp; |
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use Vcf; |
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1; |
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=head gen_tn_vcf_header |
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A string generator for generating a uniform header section for NORMAL/TUMOUR comparisons. Useful if you do not want to include the VcfTools lib. |
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@param1 wt_sample - a Sanger::CGP::Vcf::Sample object representing the wild type sample. |
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@param2 mt_sample - a Sanger::CGP::Vcf::Sample object representing the mutant type sample. |
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@param3 contigs - an array-ref of Sanger::CGP::Vcf::Contig object. |
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@param4 process_logs - an array-ref of Sanger::CGP::Vcf::VcfProcessLog objects. |
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@param5 reference_name - a String containing the name of the reference used in the VCF. |
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@param6 input_source - a String containing the name and version of the application or source of the VCF data. |
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@param7 info - an array-ref of hash-refs containing VCF formatted INFO data. |
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@param8 format - an array-ref of hash-refs containing VCF formatted FORMAT data. |
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@param9 other - an array-ref of hash-refs containing VCF formatted header data. |
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@returns - String containing a fully formatted VCF header. |
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=cut |
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sub gen_tn_vcf_header{ |
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my($wt_sample, $mt_sample, $contigs, $process_logs, $reference_name, $input_source, $info, $format, $other) = @_; |
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my $vcf = Vcf->new(version=>'4.1'); |
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init_tn_vcf_header($vcf, $wt_sample, $mt_sample, $contigs, $process_logs, $reference_name, $input_source, $info, $format, $other); |
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return $vcf->format_header(); |
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} |
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=head init_tn_vcf_header |
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Initialises the header of a Vcf object for NORMAL/TUMOUR comparisons. Useful if you do not want to include the VcfTools lib. |
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@param1 vcf - a Vcf object. |
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@param2 wt_sample - a Sanger::CGP::Vcf::Sample object representing the wild type sample. |
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@param3 mt_sample - a Sanger::CGP::Vcf::Sample object representing the mutant type sample. |
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@param4 contigs - an array-ref of Sanger::CGP::Vcf::Contig objects. |
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@param5 process_logs - an array-ref of Sanger::CGP::Vcf::VcfProcessLog objects. |
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@param6 reference_name - a String containing the name of the reference used in the VCF. |
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@param7 input_source - a String containing the name and version of the application or source of the VCF data. |
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@param8 info - an array-ref of hash-refs containing VCF formatted INFO data. |
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@param9 format - an array-ref of hash-refs containing VCF formatted FORMAT data. |
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@param10 other - an array-ref of hash-refs containing VCF formatted header data. |
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=cut |
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sub init_tn_vcf_header{ |
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my($vcf, $wt_sample, $mt_sample, $contigs, $process_logs, $reference_name, $input_source, $info, $format, $other) = @_; |
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$vcf->add_header_line( { key => 'fileDate', value => get_date() } ); |
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$vcf->add_header_line( { key => 'source', value => $input_source }, 'append' => 1 ); |
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$vcf->add_header_line( { key => 'reference', value => $reference_name } ); |
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for my $contig (@{$contigs}){ |
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add_vcf_contig($vcf,$contig) |
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} |
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for my $inf (@{$info}){ |
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$vcf->add_header_line($inf); |
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} |
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for my $for (@{$format}){ |
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$vcf->add_header_line($for); |
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} |
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for my $oth (@{$other}){ |
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$vcf->add_header_line($oth); |
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} |
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for my $process_log (@{$process_logs}){ |
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add_vcf_process_log($vcf,$process_log) |
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} |
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add_vcf_sample($vcf, $wt_sample, 'NORMAL'); |
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add_vcf_sample($vcf, $mt_sample, 'TUMOUR'); |
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} |
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=head add_vcf_sample |
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Adds a Sanger::CGP::Pindel::OutputGen::Sample object to a Vcf header object. The order of entry is important as it determines the order of the data in the resulting .vcf file. |
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@param1 vcf - a Vcf object. |
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@param2 sample - a Sanger::CGP::Vcf::Sample object. |
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@param3 id - String, the id of the sample to be displayed in the VCF file. |
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=cut |
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sub add_vcf_sample{ |
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my($vcf, $sample, $id) = @_; |
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$id = $sample->name unless defined $id and $id ne q{}; |
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my %input_hash = ( |
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key => 'SAMPLE', |
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ID => $id, |
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SampleName => $sample->name |
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); ## will use the natural order of the hash I think... |
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#push %input_hash , 'Description', $sample->description if $sample->description; |
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$input_hash{Description} = $sample->description if $sample->description; |
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$input_hash{Study} = $sample->study if $sample->study; |
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$input_hash{Source} = $sample->accession_source if $sample->accession_source; |
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$input_hash{Accession} = $sample->accession if $sample->accession; |
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$input_hash{Platform} = $sample->platform if $sample->platform; |
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$input_hash{Protocol} = $sample->seq_protocol if $sample->seq_protocol; |
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$vcf->add_header_line(\%input_hash); |
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$vcf->add_columns( $id ); |
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} |
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=head add_vcf_contig |
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Adds a Sanger::CGP::Pindel::OutputGen::Contig object to a Vcf header object. |
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@param1 vcf - a Vcf object. |
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@param2 contig - a Sanger::CGP::Vcf::Contig object. |
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=cut |
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sub add_vcf_contig{ |
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my($vcf, $contig) = @_; |
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my %input_hash = ( |
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key => 'contig', |
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ID => $contig->name, |
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assembly => $contig->assembly, |
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length => $contig->length, |
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species => $contig->species, |
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); ## will use the natural order of the hash I think... |
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$input_hash{md5} = $contig->checksum if $contig->checksum; |
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$vcf->add_header_line(\%input_hash); |
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} |
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=head add_vcf_process_log |
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Adds a Sanger::CGP::Vcf::VcfProcessLog object to a Vcf header object. |
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@param1 vcf - a Vcf object. |
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@param2 process_log - a Sanger::CGP::Pindel::OutputGen::VcfProcessLog object. |
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=cut |
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sub add_vcf_process_log{ |
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my($vcf, $process_log) = @_; |
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my %input_hash = (key => 'vcfProcessLog'); |
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$input_hash{InputVCF} = $process_log->input_vcf if $process_log->input_vcf; |
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$input_hash{InputVCFSource} = $process_log->input_vcf_source if $process_log->input_vcf_source; |
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$input_hash{InputVCFVer} = $process_log->input_vcf_ver if $process_log->input_vcf_ver; |
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$input_hash{InputVCFParam} = $process_log->input_vcf_params if $process_log->input_vcf_params; |
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$vcf->add_header_line(\%input_hash, append => 1); |
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} |
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sub get_date { |
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my @timeData = localtime(time); |
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my $year = 1900 + $timeData[5]; |
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return |
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$year |
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. sprintf( "%02d", $timeData[4]+1 ) |
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. sprintf( "%02d", $timeData[3] ); |
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} |