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Extract a random sequence from a file
By Abhi 3120 days ago
#!/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];
}
