Extract a random sequence from a file

Abhi — Thu, 12 May 2016 11:02:24 -0500

#!/usr/local/bin/perl -w

use strict;
use warnings;
use autodie;

use List::Util qw/ shuffle /;

my $outputfile = 'randomoutput.txt';

open my $in_fh,  '<', 'seq1.fa';
open my $out_fh, '>', $outputfile;

my $size       = 21;
my $count      = 10;

while (my $line = <$in_fh>) {
   next unless $line =~ /^([ATGCN]+)/;

   my $genome     = $1;
   my $len_genome = length $genome;

   my @start_points = shuffle(0 .. $len_genome-$size);
   next unless @start_points >= $count;
   print substr($genome, $_, 21), "\n" for @start_points[0 .. $count-1];
}

BOL: Owner

Extract a random sequence from a file