fakmer

#!/usr/bin/perl
# Generate tiled k-mers
# Copyright 2012 Shaun Jackman

use strict;
use Getopt::Std 'getopts';

my %opt;
getopts('k:', \%opt);
my $opt_k = $opt{'k'};

my $id;
while (<>) {
	chomp;
	if (/^>/) {
		$id = $_;
		next;
	}
	my $l = length;
	for my $i (0..($l - $opt_k)) {
		#print '>', $., ':', $i, "\n", substr($_, $i, $opt_k), "\n";
		#print $id, ':', $i, "\n", substr($_, $i, $opt_k), "\n";

		#my $seq = substr($_, $i, $opt_k);
		#if ($seq =~ /N/) {
		#	print STDERR "skipping N\n";
		#	next;
		#}
		#my ($chr, $rest) = split ':', substr $id, 1;
		#my ($pos, $comment) = split ' ', $rest;
		#my $kpos = $pos + $i;
		##my $kid = "$chr:$kpos $comment:$i\n";
		#my $kid = ">$comment:$i $chr:$kpos\n";
		#print $kid, $seq, "\n";

		my ($tag, $comment) = split ' ', $id;
		print $tag, ':', $i, , ' ', $comment, "\n",
			substr($_, $i, $opt_k), "\n";
	}
}