comparison MDSplot/MDSbasedOnIBSmatrix.pl @ 15:31c23d943c29 draft default tip

Uploaded

14:d15869b3731a

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);

my %populations;
if (-e "$in.individual_info.txt")
{
	open(my $I,"$in.individual_info.txt");

		$populations{$ind} = $pop;
	}
	close($I);
}

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);
		if ($line =~/^ /)
		{
			my $ind = $i[1];
			my $pop = "Pop1";
			#if ($ind=~/^d/){$pop="Pop2";}
			if ($populations{$ind})
			{
				$pop = $populations{$ind};
			}
			print $OUT "$pop	$ind	".$i[4]."	".$i[5]."\n";
		}
		if ($line =~/^\w/)
		{
			my $ind = $i[0];
			my $pop = "Pop1";
			#if ($ind=~/^d/){$pop="Pop2";}
			if ($populations{$ind})
			{
				$pop = $populations{$ind};
			}
			print $OUT "$pop	$ind	".$i[3]."	".$i[4]."\n";
		}
		
	}
	if (/C1/){$go = 1;}
}
close($O);
close($OUT);

15:31c23d943c29

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");

		$populations{$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);