--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admixture/Admixture.pl	Fri Feb 20 10:11:57 2015 -0500
@@ -0,0 +1,159 @@
+#!/usr/bin/perl
+
+use strict;
+use Switch;
+use Getopt::Long;
+use Bio::SeqIO;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input HAPMAP>
+    -o, --output        <output>
+    -k, --kmin          <K min. int>
+    -m, --maxK          <K max. int>
+    -d, --directory     <temporary directory>
+    -p, --path          <path to executables>
+~;
+$usage .= "\n";
+
+my ($input,$output,$kmin,$kmax,$directory,$path);
+
+
+GetOptions(
+	"input=s"      => \$input,
+	"output=s"     => \$output,
+	"kmin=s"       => \$kmin,
+	"maxK=s"       => \$kmax,
+	"directory=s"  => \$directory,
+	"path=s"       => \$path
+);
+
+
+die $usage
+  if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$path);
+
+if ($kmin =~/^(\d+)\s*$/){
+        $kmin = $1;
+}
+else{
+        die "Error: kmin must be an integer\n";
+}
+if ($kmax =~/^(\d+)\s*$/){
+        $kmax = $1;
+}
+else{
+        die "Error: kmax must be an integer\n";
+}
+
+  
+######################
+# create map file
+######################
+open(my $M,">$directory/input.map");
+open(my $H,$input);
+<$H>;
+while(<$H>)
+{
+	my @infos = split(/\t/,$_);
+	print $M $infos[2] . "\t" . $infos[0] . "\t" . "0" . "\t" . $infos[3] . "\n";
+}
+close($H);
+close($M);
+
+######################
+# create ped file
+######################
+system("$path/transpose.awk $input >$directory/input.ped.2");
+
+open(my $P,">$directory/input.ped");
+open(my $P2,"$directory/input.ped.2");
+my $n = 0;
+my $ind_num = 0;
+my @individus;
+while(<$P2>)
+{
+	$n++;
+	if ($n > 11)
+	{
+		my $line = $_;
+		$line =~s/N/0/g;
+		if (/^([^\s]+)\s+(.*)$/)
+		{
+			$ind_num++;
+			my $ind = $1;
+			push(@individus,$ind);
+			my $genoyping_line = $2;
+			print $P "$ind	$ind_num	0	0	1	2";
+			my @genotypes = split(/\s/,$genoyping_line);
+			foreach my $genotype(@genotypes)
+			{
+				$genotype =~s/N/0/g;
+				my @alleles = split("",$genotype);
+				print $P "	" . join(" ",@alleles);
+			}
+			
+			print $P "\n";
+		}
+	}
+}
+close($P2);
+close($P);
+
+unlink("$directory/input.ped.2");
+
+system("plink --file $directory/input --out $directory/out --make-bed --noweb >>$directory/plink.log 2>&1");
+
+
+###################################
+# launch admixture for different K
+###################################
+my %errors;
+for (my $k = $kmin; $k <= $kmax; $k++)
+{
+	system("admixture --cv $directory/out.bed $k >>$directory/log.$k 2>&1");
+	my $cv_error_line = `grep -h CV $directory/log.$k`;
+	if ($cv_error_line =~/: (\d+\.*\d*)$/)
+	{
+		$errors{$1} = $k;
+	}
+	system("cat $directory/log.$k >>$directory/logs");
+	system("echo '\n\n====================================\n\n' >>$directory/logs");
+	system("cat out.$k.Q >>$directory/outputs.Q");
+	system("echo '\n\n====================================\n\n' >>$directory/outputs.Q");
+	system("cat out.$k.P >>$directory/outputs.P");
+	system("echo '\n\n====================================\n\n' >>$directory/outputs.P");
+}
+
+my @sorted_errors = sort {$a<=>$b} keys(%errors);
+my $best_K = $errors{@sorted_errors[0]};
+
+
+#system("cp -rf out.$best_K.Q $directory/output");
+
+open(BEST1,"out.$best_K.Q");
+open(BEST2,">$directory/output");
+print BEST2 "<Covariate>\n";
+print BEST2 "<Trait>";
+for (my $j=1;$j<=$best_K;$j++)
+{
+	print BEST2 "	Q" . $j;
+}
+print BEST2 "\n";
+my $i = 0;
+while(<BEST1>)
+{
+	my $line = $_;
+	$line =~s/ /\t/g;
+	my $ind = $individus[$i];
+	print BEST2 "$ind	";
+	print BEST2 $line;
+	$i++;
+}
+close(BEST1);
+close(BEST2);
+
+system("cp -rf $directory/log.$best_K $directory/log");
+
+
+
+