--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hapmap2mlmm/HapmapToMLMMFiles.pl	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,117 @@
+#!/usr/bin/perl
+
+use strict;
+use Switch;
+use Getopt::Long;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -h, --hapmap       <Hapmap input file>
+    -m, --map          <Map output file>
+    -g, --geno         <Genotype output file>
+    -p, --path         <Path for transpose executable>
+~;
+$usage .= "\n";
+
+my ($hapmap,$map,$geno,$path);
+
+
+GetOptions(
+        "geno=s"       => \$geno,
+        "map=s"        => \$map,
+        "hapmap=s"     => \$hapmap,
+        "path=s"       => \$path,
+);
+
+
+die $usage
+  if ( !$geno || !$map || !$hapmap || !$path);
+  
+my $TRANSPOSE_EXE = "$path/transpose.awk";
+
+my @snps;
+my %chrom_pos;
+my $num_line = 0;
+open(my $O,">geno_transposed");
+open(my $H,$hapmap);
+while(<$H>)
+{
+	$num_line++;
+	my $line = $_;
+	chomp($line);
+	$line =~s/\r//g;
+	$line =~s/\n//g;
+	my @infos = split(/\t/,$line);
+	if ($num_line == 1)
+	{
+		print $O "Ind_id";
+		for (my $i = 11; $i <= $#infos; $i++)
+		{
+			my $individual = $infos[$i];
+			print $O "	" . $individual;
+		}
+		print $O "\n";
+	}
+	elsif ($num_line > 1)
+	{
+		my $snp = $infos[0];
+		my $variation = $infos[1];
+		my %scores;
+		if ($variation =~/(\w)\/(\w)/)
+		{
+			my $allele1 = $1;
+			my $allele2 = $2;
+			$scores{$allele1} = 0;
+			$scores{$allele2} = 1;
+		}
+		my $chrom = $infos[2];
+		my $pos = $infos[3];
+		$chrom_pos{$snp}{"chrom"} = $chrom;
+		$chrom_pos{$snp}{"pos"} = $pos;
+		push(@snps,$snp);
+		print $O "$snp";
+		for (my $i = 11; $i <= $#infos; $i++)
+		{
+			my $genotype = $infos[$i];
+			my @alleles = split("",$genotype);
+			if ($genotype ne "NN")
+			{
+				my $score = $scores{$alleles[0]} + $scores{$alleles[1]};
+				print $O "	$score";
+			}
+			else
+			{
+				print $O "	NA";
+			}
+		}
+		print $O "\n";
+	}
+}
+close($H);
+close($O);
+
+open(my $M,">$map");
+print $M "SNP	Chr	Pos\n";
+foreach my $snp(@snps)
+{
+	print $M "$snp	" . $chrom_pos{$snp}{"chrom"} . "	". $chrom_pos{$snp}{"pos"} . "\n";
+}
+close($M);
+
+system("$TRANSPOSE_EXE geno_transposed >geno_transposed2");
+
+open(my $F,">$geno");
+open(my $G,"geno_transposed2");
+while(<$G>)
+{
+	my $line = $_;
+	$line =~s/ /\t/g;
+	print $F $line;
+}
+close($G);
+close($F);
+
+unlink("geno_transposed");
+unlink("geno_transposed2");
+
+