blob: 83719502f5d3b23c40ee833ab9d5b32c8810aa9c (
plain)
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
|
#!/usr/bin/env perl
use warnings;
use Getopt::Std;
getopts('q');
$target = shift;
$source = shift;
$align = shift or die "
Usage: extract-singletons.perl target source align
";
open(TARGET,$target) or die "Error: unable to open target file \"$target\"!\n";
open(SOURCE,$source) or die "Error: unable to open source file \"$source\"!\n";
open(ALIGN,$align) or die "Error: unable to open alignment file \"$align\"!\n";
while (<TARGET>) {
unless (defined $opt_q) {
print STDERR "\r$M" if ++$M%1000 == 0;
}
@T = split;
$_ = <SOURCE>;
@S = split;
$_ = <ALIGN>;
@A = split;
my(@source_links,@target_links);
for( $i=0; $i<=$#A; $i+=2 ) {
$target_links[$A[$i]]++;
$source_links[$A[$i+1]]++;
}
for( $i=0; $i<=$#A; $i+=2 ) {
if ($target_links[$A[$i]] == 1 && $source_links[$A[$i+1]] == 1 &&
$T[$A[$i]] eq $S[$A[$i+1]])
{
$count{$S[$A[$i+1]]}++; # Print this if it only occurs here
}
else {
$count{$S[$A[$i+1]]}+=2; # Don't print this
}
}
}
foreach $w (sort keys %count) {
print "$w\n" if $count{$w}==1;
}
|