|
1
|
1 #!/usr/bin/perl
|
|
|
2
|
|
|
3 use strict;
|
|
|
4 use Switch;
|
|
|
5 use Getopt::Long;
|
|
|
6 use Bio::SeqIO;
|
|
|
7
|
|
|
8 my $PLINK_EXE= "/apps/www/sniplay.cirad.fr/tools/plink/plink-1.07-x86_64/plink";
|
|
|
9
|
|
|
10 my $usage = qq~Usage:$0 <args> [<opts>]
|
|
|
11 where <args> are:
|
|
|
12 -i, --in <input>
|
|
|
13 -o, --out <output>
|
|
|
14 ~;
|
|
|
15 $usage .= "\n";
|
|
|
16
|
|
|
17 my ($in,$out);
|
|
|
18
|
|
|
19
|
|
|
20 GetOptions(
|
|
|
21 "in=s" => \$in,
|
|
|
22 "out=s" => \$out
|
|
|
23 );
|
|
|
24
|
|
|
25 die $usage
|
|
|
26 if ( !$in || !$out);
|
|
|
27
|
|
|
28
|
|
|
29 my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1";
|
|
|
30 system($plink_command);
|
|
|
31
|
|
|
32 my $awk_cmd = "awk \{\'print \$1\'\} $in.ped";
|
|
|
33 my $inds = `$awk_cmd`;
|
|
|
34 my @individuals = split("\n",$inds);
|
|
|
35
|
|
|
36
|
|
|
37 open(my $OUT,">$out.mds_plot.txt");
|
|
|
38 my $go = 0;
|
|
|
39 open(my $O,"$out.mds");
|
|
|
40 while(<$O>)
|
|
|
41 {
|
|
|
42 if ($go)
|
|
|
43 {
|
|
|
44 my $line = $_;
|
|
|
45 $line =~s/\n//g;
|
|
|
46 $line =~s/\r//g;
|
|
|
47 my @i = split(/\s+/,$line);
|
|
|
48 my $ind = $i[1];
|
|
|
49 print $OUT "$ind ".$i[4]." ".$i[5]."\n";
|
|
|
50 }
|
|
|
51 if (/C1/){$go = 1;}
|
|
|
52 }
|
|
|
53 close($O);
|
|
|
54 close($OUT);
|
|
|
55
|
|
|
56
|
|
|
57 my $j = 0;
|
|
|
58 open(my $IBS,">$out.ibs_matrix.txt");
|
|
|
59 print $IBS "Individuals " . join("\t",@individuals)."\n";
|
|
|
60 open(my $O2,"$out.mibs");
|
|
|
61 while(<$O2>)
|
|
|
62 {
|
|
|
63 my $line = $_;
|
|
|
64 $line =~s/\n//g;
|
|
|
65 $line =~s/\r//g;
|
|
|
66 my @i = split(/\s+/,$line);
|
|
|
67 print $IBS $individuals[$j]. " ". join("\t",@i)."\n";
|
|
|
68 $j++;
|
|
|
69 }
|
|
|
70 close($O2);
|
|
|
71 close($IBS);
|
|
|
72
|
|
|
73
|
|
|
74
|
|
|
75
|
|
|
76
|
|
|
77
|
