--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_analysis_conversion/gd_snp2vcf.pl	Tue May 28 17:01:14 2013 -0400
@@ -0,0 +1,197 @@
+#!/usr/bin/perl -w
+use strict;
+
+#convert from gd_snp file to vcf file (with dbSNP fields)
+
+#gd_snp table format:
+#1. chr
+#2. position (0 based)
+#3. ref allele
+#4. second allele
+#5. overall quality
+#foreach individual (6-9, 10-13, ...)
+#a. count of allele in 3
+#b. count of allele in 4
+#c. genotype call (-1, or count of ref allele)
+#d. quality of genotype call (quality of non-ref allele from masterVar)
+
+if (!@ARGV) {
+   print "usage: gd_snp2vcf.pl file.gd_snp[.gz|.bz2] -geno=8[,12:16,20...] -handle=HANDLE -batch=BATCHNAME -ref=REFERENCEID [-bioproj=XYZ -biosamp=ABC -pop=POPID[,POPID2...] -chrCol=9 -posCol=9 ] > snpsForSubmission.vcf\n";
+   exit;
+}
+
+my $in = shift @ARGV;
+my $genoCols = '';
+my $handle;
+my $batch;
+my $bioproj;
+my $biosamp;
+my $ref;
+my $pop;
+my $cr = 0; #allow to use alternate reference?
+my $cp = 1;
+my $meta;
+foreach (@ARGV) {
+   if (/-geno=([0-9,]+)/) { $genoCols .= "$1:"; }
+   elsif (/-handle=(.*)/) { $handle = $1; }
+   elsif (/-batch=(.*)/) { $batch = $1; }
+   elsif (/-bioproj=(.*)/) { $bioproj = $1; }
+   elsif (/-biosamp=(.*)/) { $biosamp = $1; }
+   elsif (/-ref=(.*)/) { $ref = $1; } 
+   elsif (/-population=(\S+)/) { $pop = $1; }
+   elsif (/-chrCol=(\d+)/) { $cr = $1 - 1; }
+   elsif (/-posCol=(\d+)/) { $cp = $1 - 1; }
+   elsif (/-metaOut=(.*)/) { $meta = $1; }
+}
+if ($cr < 0 or $cp < 0) { die "ERROR the column numbers should be 1 based.\n"; }
+ 
+#remove trailing delimiters
+$genoCols =~ s/,:/:/g;
+$genoCols =~ s/[,:]$//;
+
+my @gnc = split(/,|:/, $genoCols);
+
+if ($in =~ /.gz$/) { 
+   open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
+}elsif ($in =~ /.bz2$/) {
+   open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n";
+}else {
+   open(FH, $in) or die "Couldn't open $in, $!\n";
+}
+my @head = prepHeader();
+if (@head) { 
+   print join("\n", @head), "\n";
+   #now column headers
+   print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
+   if (defined $pop) { 
+      $pop =~ s/,$//;
+      my $t = $pop;
+      $t =~ s/,/\t/g;
+      print "\tFORMAT\t$t";
+   }
+   print "\n";
+}
+while (<FH>) {
+   chomp;
+   if (/^#/) { next; }
+   if (/^\s*$/) { next; } 
+   my @f = split(/\t/);
+   #vcf columns: chrom pos id ref alt qual filter info
+   # info must have VRT=[0-9] 1==SNV 2=indel 6=NoVariation 8=MNV ...
+   my $vrt = 1;
+   if ($f[2] !~ /^[ACTG]$/ or $f[3] !~ /^[ACTG]$/) {
+      die "Sorry this can only do SNV's at this time\n";
+   }
+   if (scalar @gnc == 1) { #single genotype column
+      if (!defined $f[4] or $f[4] == -1) { $f[4] = '.'; }
+      if ($f[$gnc[0]-1] == 2) { $vrt = 6; } #reference match
+      print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n";
+      #TODO? put read counts in comment?
+   }elsif ($pop) { #do as population
+      my @cols;
+      foreach my $gp (split(/:/,$genoCols)) { #foreach population
+         my @g = split(/,/, $gp);
+         my $totChrom = 2*(scalar @g);
+         my $totRef = 0;
+         foreach my $i (@g) { if ($f[$i-1] == -1) { next; } $totRef += $f[$i-1]; }
+         if ($totChrom == $totRef) { $vrt = 6; }
+         if ($totRef > $totChrom) { die "ERROR likely the wrong column was chosen for genotype\n"; }
+         my $altCnt = $totChrom - $totRef;
+         push(@cols, "$totChrom:$altCnt");
+      }
+      print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\tNA:AC\t", join("\t", @cols), "\n";
+   }else { #leave allele counts off
+      my $totChrom = 2*(scalar @gnc);
+      my $totRef = 0;
+      foreach my $i (@gnc) { if ($f[$i-1] == -1) { next; } $totRef += $f[$i-1]; }
+      if ($totChrom == $totRef) { $vrt = 6; }
+      print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n";
+   }
+}
+close FH or die "Couldn't close $in, $!\n";
+
+if ($meta) {
+   open(FH, ">", $meta) or die "Couldn't open $meta, $!\n";
+   print FH "TYPE: CONT\n",
+            "HANDLE: $handle\n",
+            "NAME: \n",
+            "FAX: \n",
+            "TEL: \n",
+            "EMAIL: \n",
+            "LAB: \n",
+            "INST: \n",
+            "ADDR: \n",
+            "||\n",
+            "TYPE: METHOD\n",
+            "HANDLE: $handle\n",
+            "ID: \n",
+            "METHOD_CLASS: Sequence\n",
+            "TEMPLATE_TYPE: \n",
+            "METHOD:\n",
+            "||\n";
+   if ($pop) {
+      my @p = split(/,/, $pop);
+      foreach my $t (@p) {
+         print FH
+            "TYPE: POPULATION\n",
+            "HANDLE: $handle\n", 
+            "ID: $t\n", 
+            "POPULATION: \n", 
+            "||\n";
+      }
+   }
+   print FH "TYPE: SNPASSAY\n",
+            "HANDLE: $handle\n",
+            "BATCH: $batch\n",
+            "MOLTYPE: \n",
+            "METHOD: \n",
+            "ORGANISM: \n",
+            "||\n",
+            "TYPE: SNPPOPUSE | SNPINDUSE\n",
+            "HANDLE: $handle\n",
+            "BATCH: \n",
+            "METHOD: \n",
+            "||\n";
+
+   close FH or die "Couldn't close $meta, $!\n";
+}
+
+exit 0;
+
+#parse old header and add or create new
+sub prepHeader {
+   my @h;
+   $h[0] = '##fileformat=VCFv4.1';
+   my ($day, $mo, $yr) = (localtime)[3,4,5];
+   $mo++;
+   $yr+=1900;
+   $h[1] = '##fileDate=' . "$yr$mo$day";
+   $h[2] = "##handle=$handle";
+   $h[3] = "##batch=$batch";
+   my $i = 4;
+   if ($bioproj) { $h[$i] = "##bioproject_id=$bioproj";  $i++; }
+   if ($biosamp) { $h[$i] = "##biosample_id=$biosamp"; $i++; }
+   $h[$i] = "##reference=$ref";  ##reference=GCF_999999.99
+   #$i++;
+   #$h[$i] = '##INFO=<ID=LID, Number=1,Type=string, Description="Unique local variation ID or name for display. The LID provided here combined with the handle must be unique for a particular submitter.">'
+   $i++;
+   $h[$i] = '##INFO=<ID=VRT,Number=1,Type=Integer,Description="Variation type,1 - SNV: single nucleotide variation,2 - DIV: deletion/insertion variation,3 - HETEROZYGOUS: variable, but undefined at nucleotide level,4 - STR: short tandem repeat (microsatellite) variation, 5 - NAMED: insertion/deletion variation of named repetitive element,6 - NO VARIATON: sequence scanned for variation, but none observed,7 - MIXED: cluster contains submissions from 2 or more allelic classes (not used) ,8 - MNV: multiple nucleotide variation with all eles of common length greater than 1,9 - Exception">';
+   #sometimes have allele freqs?
+   if (defined $pop) {
+      $i++;
+      $h[$i] = "##FORMAT=<ID=NA,Number=1,Type=Integer,Description=\"Number of alleles for the population.\"";
+      $i++;
+      $h[$i] = '##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count for each alternate allele.">';
+      my @p = split(/,/, $pop);
+      foreach my $t (@p) {
+         $i++;
+         $h[$i] = "##population_id=$t";
+      }
+   }
+   #PMID?
+##INFO=<ID=PMID,Number=.,Type=Integer,Description="PubMed ID linked to variation if available.">
+
+   return @h;
+}
+####End
+