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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
use Ktree;
use Nuc_translator;
my $usage = "usage: $0 fasta_file KmerSize [DSmode]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $kmer_length = $ARGV[1] or die $usage;
my $DS_mode = $ARGV[2] || 0;
main: {
my $ktree = new Ktree();
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $seq = $seq_obj->get_sequence();
my @chars = split(//, $seq);
for (my $i = 0; $i <= length($seq) - $kmer_length; $i++) {
my $kmer = join("", @chars[$i..($i+$kmer_length-1)]);
$ktree->add_kmer($kmer);
if ($DS_mode) {
$ktree->add_kmer( &reverse_complement($kmer) );
}
}
}
$ktree->report_kmer_counts();
exit(0);
}
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