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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fa [kmer_length=25]\n\n";
my $fa_file = $ARGV[0] or die $usage;
my $kmer_length = $ARGV[1] || 25;
main: {
my $fasta_reader = new Fasta_reader($fa_file);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = $seq_obj->get_sequence();
for (my $i = 0; $i < length($sequence) - $kmer_length + 1; $i++) {
my $kmer = substr($sequence, $i, $kmer_length);
print "$kmer\n";
}
}
exit(0);
}
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