--- a/MDSbasedOnIBSmatrix.pl	Tue Jan 08 08:45:34 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Getopt::Long;
-use Bio::SeqIO;
-
-my $PLINK_EXE= "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 . " --vcf  $in --cluster  --allow-extra-chr --matrix --mds-plot 3 --out $out >>$in.plink.log 2>&1";
-system($plink_command);
-
-my @individuals = ();
-
-my %populations;
-if (-e "$in.individual_info.txt")
-{
-	open(my $I,"$in.individual_info.txt");
-	while(<$I>)
-	{
-		my $line = $_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		my ($ind,$pop) = split(/;/,$line);
-		$populations{$ind} = $pop;
-	}
-	close($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)
-	{
-		my $line = $_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		my @i = split(/\s+/,$line);
-		if ($line =~/^ /)
-		{
-			#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]."	".$i[5]."	".$i[6]."\n";
-		}
-		if ($line =~/^\w/)
-		{
-			#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]."	".$i[4]."	".$i[5]."\n";
-		}
-		$numline++;		
-	}
-	if (/C1/){$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);
-
-
-	
-	
-
-