annotate kmersvm/kmer2meme.pl @ 7:fd740d515502 draft default tip

Uploaded revised kmer-SVM to include modules from kmer-visual.

use strict;

open(my $w_fh, "<", $ARGV[0]);
my $num_kmers = $ARGV[1];
my @weights = <$w_fh>;

my @temp_k = @weights[8..(7+$num_kmers), (-$num_kmers..-1)];

my @kmers = ();
#cleanup kmers
for my $i (0..($#temp_k)){
	my @temp = split('\t',$temp_k[$i]);
	#modified by dongwon 042713
	#push(@kmers, ($temp[0], $temp[1]));
	push(@kmers, $temp[0]);
}

open(my $o_fh, ">", "kmer2meme.meme");

print $o_fh
"MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies (from no specific genome):
A 0.25 C 0.25 G 0.25 T 0.25\n\n";

foreach my $kmer (@kmers) {
	print $o_fh "MOTIF $kmer\n";
	my $l = length($kmer);
	print $o_fh "letter-probability matrix: alength= 4 w= $l nsites= 1 E= 0\n";
	foreach my $i (0..($l-1)) {
		my $nc = substr($kmer, $i, 1);
		if ($nc eq "A") {
			print $o_fh " 1.00  0.00  0.00  0.00\n";
		}elsif ($nc eq "C") {
			print $o_fh " 0.00  1.00  0.00  0.00\n";
		}elsif ($nc eq "G") {
			print $o_fh " 0.00  0.00  1.00  0.00\n";
		}elsif ($nc eq "T") {
			print $o_fh " 0.00  0.00  0.00  1.00\n";
		}else {
			print " 0.25  0.25  0.25  0.25\n";
		}
	}
	print $o_fh "\n";
}