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