1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../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);
}
|
