--- a/MDSplot/MDSbasedOnIBSmatrix.pl	Tue Jan 08 08:46:57 2019 -0500
+++ b/MDSplot/MDSbasedOnIBSmatrix.pl	Tue Jan 08 08:47:56 2019 -0500
@@ -25,12 +25,10 @@
   if ( !$in || !$out);
   
 	
-my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1";
+my $plink_command = $PLINK_EXE . " --vcf  $in --cluster  --allow-extra-chr --matrix --mds-plot 3 --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);
+my @individuals = ();
 
 my %populations;
 if (-e "$in.individual_info.txt")
@@ -47,9 +45,19 @@
 	close($I);
 }
 
+
+my $line_ind = `grep CHROM $in`;
+$line_ind =~s/\n//g;$line_ind =~s/\r//g;
+my @tab = split(/\t/,$line_ind);
+for (my $i = 9; $i <= $#tab; $i++){
+	push(@individuals,$tab[$i]);
+}
+
 open(my $OUT,">$out.mds_plot.txt");
 my $go = 0;
+print $OUT "Pop	sample	val1	val2	val3\n";
 open(my $O,"$out.mds");
+my $numline = 0;
 while(<$O>)
 {
 	if ($go)
@@ -60,27 +68,29 @@
 		my @i = split(/\s+/,$line);
 		if ($line =~/^ /)
 		{
-			my $ind = $i[1];
+			#my $ind = $i[1];
+			my $ind = $individuals[$numline];
 			my $pop = "Pop1";
 			#if ($ind=~/^d/){$pop="Pop2";}
 			if ($populations{$ind})
 			{
 				$pop = $populations{$ind};
 			}
-			print $OUT "$pop	$ind	".$i[4]."	".$i[5]."\n";
+			print $OUT "$pop	$ind	".$i[4]."	".$i[5]."	".$i[6]."\n";
 		}
 		if ($line =~/^\w/)
 		{
-			my $ind = $i[0];
+			#my $ind = $i[0];
+			my $ind = $individuals[$numline];
 			my $pop = "Pop1";
 			#if ($ind=~/^d/){$pop="Pop2";}
 			if ($populations{$ind})
 			{
 				$pop = $populations{$ind};
 			}
-			print $OUT "$pop	$ind	".$i[3]."	".$i[4]."\n";
+			print $OUT "$pop	$ind	".$i[3]."	".$i[4]."	".$i[5]."\n";
 		}
-		
+		$numline++;		
 	}
 	if (/C1/){$go = 1;}
 }