From 23b5d71e76c8acd08046256f0fb8a36a08a6b057 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 11 Aug 2010 00:20:08 +0000
Subject: [PATCH] A quickly hacked together replacement for
 AnnotateVCFwithMAF.py, which doesn't work anymore with Cancer's updated
 annotator.  Takes an annotated MAF file and imports the annotations into the
 VCF file.  For the MAF annotator's DNP and TNP annotations (which I think are
 likely to not be correct, given the lack of phasing information or even
 proper association to the same sample), just propagate the annotation from
 the previous annotated variant to which the multinucleotide polymorphism was
 associated.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4007 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/AnnotateVCFwithMAF.pl | 122 +++++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100755 perl/AnnotateVCFwithMAF.pl

diff --git a/perl/AnnotateVCFwithMAF.pl b/perl/AnnotateVCFwithMAF.pl
new file mode 100755
index 000000000..1e5dc2363
--- /dev/null
+++ b/perl/AnnotateVCFwithMAF.pl
@@ -0,0 +1,122 @@
+#!/usr/bin/perl -w
+
+use strict;
+use lib "$ENV{'STING_DIR'}/perl";
+use StingArgs;
+use Data::Dumper;
+
+my %args = &getCommandArguments("VCF_IN" => undef, "MAF_IN" => undef, "VCF_OUT" => "/dev/stdout");
+
+my %ignoreEntries = (
+    'normal_barcode' => 1,
+    'tumor_barcode' => 1,
+    'build' => 1,
+    'tum_allele1' => 1,
+    'ref_allele' => 1,
+    'tum_allele2' => 1,
+    'start' => 1,
+    'end' => 1,
+);
+
+my %maf;
+open(MAF_IN, $args{'MAF_IN'});
+
+chomp(my $mafheader = <MAF_IN>);
+chomp($mafheader);
+my @mafheader = split(/\s+/, $mafheader);
+
+while (my $mafline = <MAF_IN>) {
+    chomp($mafline);
+    my @mafline = split(/\s+/, $mafline);
+
+    my %mafentry;
+    for (my $i = 0; $i <= $#mafheader; $i++) {
+        $mafentry{$mafheader[$i]} = $mafline[$i];
+    }
+
+    my $locus = "$mafentry{'chr'}:$mafentry{'start'}";
+    if (exists($mafentry{$locus})) {
+        print "Locus $locus already spoken for!\n";
+        print Dumper(\%mafentry);
+        exit(1);
+    }
+
+    $maf{$locus} = \%mafentry;
+
+    #print Dumper(\%mafentry);
+}
+close(MAF_IN);
+
+open(VCF_OUT, ">$args{'VCF_OUT'}");
+open(VCF_IN, $args{'VCF_IN'});
+
+my @vcfheader;
+while (my $vcfline = <VCF_IN>) {
+    chomp($vcfline);
+
+    if ($vcfline =~ /##/) {
+        print VCF_OUT "$vcfline\n";
+    } elsif ($vcfline =~ /#CHROM/) {
+        print VCF_OUT "##source=AnnotateVCFwithMAF\n";
+        print VCF_OUT "##INFO=cDNAchange,1,String,cDNAchange\n";
+        print VCF_OUT "##INFO=classification,1,String,classification\n";
+        print VCF_OUT "##INFO=codonchange,1,String,codonchange\n";
+        print VCF_OUT "##INFO=gene,1,String,gene\n";
+        print VCF_OUT "##INFO=genomechange,1,String,genomechange\n";
+        print VCF_OUT "##INFO=proteinchange,1,String,proteinchange\n";
+        print VCF_OUT "##INFO=strand,1,String,strand\n";
+        print VCF_OUT "##INFO=transcript,1,String,transcript\n";
+        print VCF_OUT "##INFO=type,1,String,type\n";
+        print VCF_OUT "$vcfline\n";
+
+        $vcfline =~ s/#//g;
+        @vcfheader = split(/\s+/, $vcfline);
+    } else {
+        my @vcfentry = split(/\s+/, $vcfline);
+        my %vcfentry;
+
+        for (my $i = 0; $i <= $#vcfheader; $i++) {
+            $vcfentry{$vcfheader[$i]} = $vcfentry[$i];
+        }
+
+        my $locus = "$vcfentry{'CHROM'}:$vcfentry{'POS'}";
+        if (!exists($maf{$locus})) {
+            for (my $i = 1; $i <= 10; $i++) {
+                $locus = "$vcfentry{'CHROM'}:" . ($vcfentry{'POS'}-$i);
+
+                last if (exists($maf{$locus}));
+            }
+        }
+        my %mafentry = %{$maf{$locus}};
+
+        my @info = split(/;/, $vcfentry{'INFO'});
+        my %info;
+        foreach my $info (@info) {
+            my ($key, $value) = split(/=/, $info);
+
+            $info{$key} = $value;
+        }
+
+        foreach my $mafkey (sort { $a cmp $b } keys(%mafentry)) {
+            if (!$ignoreEntries{$mafkey}) {
+                $info{$mafkey} = $mafentry{$mafkey};
+            }
+        }
+
+        my @newinfo;
+        foreach my $infokey (sort { $a cmp $b } keys(%info)) {
+            push(@newinfo, "$infokey=$info{$infokey}");
+        }
+        $vcfentry{'INFO'} = join(";", @newinfo);
+
+        my @newvcfline;
+        for (my $i = 0; $i <= $#vcfheader; $i++) {
+            push(@newvcfline, $vcfentry{$vcfheader[$i]});
+        }
+
+        print VCF_OUT join("\t", @newvcfline) . "\n";
+    }
+}
+
+close(VCF_IN);
+close(VCF_OUT);