--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MDSplot/MDSbasedOnIBSmatrix.pl.org	Fri Jul 10 10:38:43 2015 -0400
@@ -0,0 +1,77 @@
+#!/usr/bin/perl
+
+use strict;
+use Switch;
+use Getopt::Long;
+use Bio::SeqIO;
+
+my $PLINK_EXE= "/apps/www/sniplay.cirad.fr/tools/plink/plink-1.07-x86_64/plink";
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --in         <input>
+    -o, --out        <output>
+~;
+$usage .= "\n";
+
+my ($in,$out);
+
+
+GetOptions(
+	"in=s"        => \$in,
+	"out=s"       => \$out
+);
+
+die $usage
+  if ( !$in || !$out);
+  
+	
+my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1";
+system($plink_command);
+
+my $awk_cmd = "awk \{\'print \$1\'\} $in.ped";
+my $inds = `$awk_cmd`;
+my @individuals = split("\n",$inds);
+
+
+open(my $OUT,">$out.mds_plot.txt");
+my $go = 0;
+open(my $O,"$out.mds");
+while(<$O>)
+{
+	if ($go)
+	{
+		my $line = $_;
+		$line =~s/\n//g;
+		$line =~s/\r//g;
+		my @i = split(/\s+/,$line);
+		my $ind = $i[1];
+		print $OUT "$ind	".$i[4]."	".$i[5]."\n";
+	}
+	if (/C1/){$go = 1;}
+}
+close($O);
+close($OUT);
+
+
+my $j = 0;
+open(my $IBS,">$out.ibs_matrix.txt");
+print $IBS "Individuals	" . join("\t",@individuals)."\n";
+open(my $O2,"$out.mibs");
+while(<$O2>)
+{
+	my $line = $_;
+	$line =~s/\n//g;
+	$line =~s/\r//g;
+	my @i = split(/\s+/,$line);
+	print $IBS $individuals[$j]. "	". join("\t",@i)."\n";
+	$j++;
+}
+close($O2);
+close($IBS);
+
+
+	
+	
+
+