File: omp_iworm_thread_contigs_to_fa.pl

package info (click to toggle)
trinityrnaseq 2.11.0%2Bdfsg-6
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 417,528 kB
  • sloc: perl: 48,420; cpp: 17,749; java: 12,695; python: 3,124; sh: 1,030; ansic: 983; makefile: 688; xml: 62
file content (35 lines) | stat: -rwxr-xr-x 556 bytes parent folder | download | duplicates (4) 
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
 
#!/usr/bin/env perl

use strict;
use warnings;

my $usage = "usage: $0 tmp.iworm.thread.txt\n\n";

my $file = $ARGV[0] or die $usage;

main: {
    open (my $fh, $file) or die $!;
    
    my $seq_counter = 0;
  reader:
    while (1) {
        
        my @vals;
        for (1..4) {
            my $line = <$fh>;
            if (eof($fh)) { last reader; }
            chomp $line;
            push (@vals, $line);
        }

        $seq_counter++;

        my $seq = pop @vals;
        print ">s$seq_counter\n$seq\n";

    }
    
    exit(0);
}