128 lines
3.4 KiB
Perl
Executable File
128 lines
3.4 KiB
Perl
Executable File
#!/usr/bin/perl -w
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use strict;
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sub usage {
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print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n";
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print "This program takes an annotated MAF file and propagates the annotations to the VCF file.\n";
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exit(1);
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}
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my %args;
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($args{'VCF_IN'}, $args{'MAF_IN'}, $args{'VCF_OUT'}) = @ARGV;
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if (!defined($args{'VCF_IN'}) || !defined($args{'MAF_IN'}) || !defined($args{'VCF_OUT'})) {
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&usage();
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}
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my %ignoreEntries = (
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'normal_barcode' => 1,
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'tumor_barcode' => 1,
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'build' => 1,
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'tum_allele1' => 1,
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'ref_allele' => 1,
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'tum_allele2' => 1,
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'start' => 1,
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'end' => 1,
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);
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my %maf;
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open(MAF_IN, $args{'MAF_IN'});
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chomp(my $mafheader = <MAF_IN>);
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chomp($mafheader);
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my @mafheader = split(/\s+/, $mafheader);
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while (my $mafline = <MAF_IN>) {
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chomp($mafline);
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my @mafline = split(/\s+/, $mafline);
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my %mafentry;
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for (my $i = 0; $i <= $#mafheader; $i++) {
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$mafentry{$mafheader[$i]} = $mafline[$i];
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}
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my $locus = "$mafentry{'chr'}:$mafentry{'start'}";
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if (exists($mafentry{$locus})) {
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print "Locus $locus already spoken for!\n";
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exit(1);
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}
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$maf{$locus} = \%mafentry;
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}
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close(MAF_IN);
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open(VCF_OUT, ">$args{'VCF_OUT'}");
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open(VCF_IN, $args{'VCF_IN'});
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my @vcfheader;
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while (my $vcfline = <VCF_IN>) {
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chomp($vcfline);
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if ($vcfline =~ /##/) {
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print VCF_OUT "$vcfline\n";
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} elsif ($vcfline =~ /#CHROM/) {
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print VCF_OUT "##source=AnnotateVCFwithMAF\n";
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print VCF_OUT "##INFO=cDNAchange,1,String,cDNAchange\n";
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print VCF_OUT "##INFO=classification,1,String,classification\n";
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print VCF_OUT "##INFO=codonchange,1,String,codonchange\n";
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print VCF_OUT "##INFO=gene,1,String,gene\n";
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print VCF_OUT "##INFO=genomechange,1,String,genomechange\n";
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print VCF_OUT "##INFO=proteinchange,1,String,proteinchange\n";
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print VCF_OUT "##INFO=strand,1,String,strand\n";
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print VCF_OUT "##INFO=transcript,1,String,transcript\n";
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print VCF_OUT "##INFO=type,1,String,type\n";
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print VCF_OUT "$vcfline\n";
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$vcfline =~ s/#//g;
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@vcfheader = split(/\s+/, $vcfline);
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} else {
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my @vcfentry = split(/\s+/, $vcfline);
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my %vcfentry;
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for (my $i = 0; $i <= $#vcfheader; $i++) {
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$vcfentry{$vcfheader[$i]} = $vcfentry[$i];
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}
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my $locus = "$vcfentry{'CHROM'}:$vcfentry{'POS'}";
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if (!exists($maf{$locus})) {
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for (my $i = 1; $i <= 10; $i++) {
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$locus = "$vcfentry{'CHROM'}:" . ($vcfentry{'POS'}-$i);
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last if (exists($maf{$locus}));
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}
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}
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my %mafentry = %{$maf{$locus}};
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my @info = split(/;/, $vcfentry{'INFO'});
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my %info;
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foreach my $info (@info) {
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my ($key, $value) = split(/=/, $info);
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$info{$key} = $value;
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}
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foreach my $mafkey (sort { $a cmp $b } keys(%mafentry)) {
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if (!$ignoreEntries{$mafkey}) {
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$info{$mafkey} = $mafentry{$mafkey};
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}
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}
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my @newinfo;
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foreach my $infokey (sort { $a cmp $b } keys(%info)) {
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push(@newinfo, "$infokey=$info{$infokey}");
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}
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$vcfentry{'INFO'} = join(";", @newinfo);
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my @newvcfline;
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for (my $i = 0; $i <= $#vcfheader; $i++) {
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push(@newvcfline, $vcfentry{$vcfheader[$i]});
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}
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print VCF_OUT join("\t", @newvcfline) . "\n";
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}
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}
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close(VCF_IN);
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close(VCF_OUT);
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