PSReliP/psrelip_pipeline/program_files/perl_programs/ps_pl2_pvar_edit.pl at main · solelena/PSReliP · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
#/usr/bin/perl
use strict;
use warnings;

my $in_file_name = $ARGV[0];
my $out_file_name = $ARGV[1];
my $line;
my $line2;
my $header_line_no = 0;

open(my $fin, '<', $in_file_name) or die($!);
my $l = 1;
while(defined ($line = <$fin>)){
  chomp ($line);
  my @fields = split(/\t/, $line);
  if ($fields[0] eq "#CHROM") {
    $header_line_no = $l;
    last;
  }
  $l++;
}
close $fin;

my $bim_col_nu = 0;
if ($header_line_no == 0) {
  open(my $fin2, '<', $in_file_name) or die($!);
  my $l3 = 1;
  my $line3;
  while(defined ($line3 = <$fin2>)){
    if ($l3 == 1) {
      chomp ($line3);
      my @fields = split(/\t/, $line3);
      $bim_col_nu = $#fields + 1;
      last;
    }
    $l3++;
  }
  close $fin2;
}

open (my $fout, q{>>}, $out_file_name) or die($!);

open(my $fin3, '<', $in_file_name) or die($!);
my $l2 = 1;
while(defined ($line2 = <$fin3>)){
  if ($header_line_no == 0) {
    chomp ($line2);
    my @fields = split(/\t/, $line2);
    my $variant_id = "";
    if ($bim_col_nu == 5) {
      if ($fields[1] eq ".") {
        $variant_id = $fields[0].":".$fields[2];
      } else {
        $variant_id = $fields[1];
      }
      print $fout $fields[0]."	".$variant_id."	".$fields[2]."	".$fields[3]."	".$fields[4]."\n";
    } elsif ($bim_col_nu == 6) {
      if ($fields[1] eq ".") {
        $variant_id = $fields[0].":".$fields[3];
      } else {
        $variant_id = $fields[1];
      }
      print $fout $fields[0]."	".$variant_id."	".$fields[2]."	".$fields[3]."	".$fields[4]."	".$fields[5]."\n";
    }
  } else {
    if ($l2 <= $header_line_no) {
      print $fout $line2;
    } else {
      chomp ($line2);
      my @fields = split(/\t/, $line2);
      my $variant_id = "";
      if ($fields[2] eq ".") {
        $variant_id = $fields[0].":".$fields[1];
      } else {
        $variant_id = $fields[2];
      }
      my $line_out = $fields[0]."	".$fields[1]."	".$variant_id;
      for (my $i=3; $i <= $#fields; $i++ ) {
        $line_out .= "	".$fields[$i];
      }
      print $fout $line_out."\n";
    }
  }
  $l2++;
}
close $fin3;

close $fout;

1;