seqare/mergeMutFiles.pl at master · ruping/seqare · 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
use strict;

my $files = shift;
my $headern = shift;

if ($headern eq ''){
  print STDERR "no header number provided, now assume \^\# as default header lines.\n";
  $headern = -1;
}

my @files;
if ($files =~ /,/){
  @files = split(',', $files);
} else {  # an file of filenames
  open FF, "$files";
  while ( <FF> ) {
    chomp;
    push (@files, $_);
  }
  close FF;
}

my $fc = 1;
foreach my $file (@files) {
  if ($fc == 1) {
    open IN, "$file";
    while ( <IN> ) {
      print "$_";
    }
    close IN;
  } else {
    my $hc = 0;
    open IN, "$file";
    while ( <IN> ) {
      $hc ++;
      if ($headern >= 0) {
        if ($hc <= $headern){
          next;
        } else {
          print "$_" if ($_ ne '');
        }
      } elsif ($headern == -1) {
        if ($_ =~ /^#/){
          next;
        } else {
          print "$_" if ($_ ne '');
        }
      }
    }
    close IN;
  }
  $fc ++;
}

exit;