File: get_Trinity_gene_to_trans_map.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 (28 lines) | stat: -rwxr-xr-x 523 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
 
#!/usr/bin/env perl

use strict;
use warnings;


while (<>) {
    if (/>(\S+)/) {
        my $acc = $1;
        if ($acc =~ /^(.*c\d+_g\d+)(_i\d+)/) {
            my $gene = $1;
            my $trans = $1 . $2;

            print "$gene\t$trans\n";
        }
        elsif ($acc =~ /^(.*comp\d+_c\d+)/) {
            my $gene = $1;
            my $trans = $acc;
            print "$gene\t$trans\n";
        }
        else {
            print STDERR "WARNING: cannot decipher accession $acc\n";
        }
    }
}

exit(0);