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Changeset 14:d15869b3731a (2019-01-08)

Previous changeset 13:734a3572c1d6 (2019-01-08) Next changeset 15:31c23d943c29 (2019-01-08)

Commit message:
Deleted selected files

removed:
MDSbasedOnIBSmatrix.pl

diff -r 734a3572c1d6 -r d15869b3731a MDSbasedOnIBSmatrix.pl
--- 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);
-
-
-
-
-
-