File: get_transcript_lengths.pl

package info (click to toggle)
trinityrnaseq 2.15.2%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid
  • size: 468,004 kB
  • sloc: perl: 49,905; cpp: 17,993; java: 12,489; python: 3,282; sh: 1,989; ansic: 985; makefile: 717; xml: 62
file content (32 lines) | stat: -rwxr-xr-x 505 bytes parent folder | download | duplicates (3) 
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
 
#!/usr/bin/env perl

use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;


my $usage = "usage: $0 transcripts.fasta\n\n";

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

main: {
    
    my $fasta_reader = new Fasta_reader($trans_fasta);
    
    while (my $seq_obj = $fasta_reader->next()) {

        my $acc = $seq_obj->get_accession();
        my $seq = $seq_obj->get_sequence();

        print join("\t", $acc, length($seq)) . "\n";
    }


    exit(0);
}