use strict;
use warnings;

# usage: script.pl {motif_width} {dnafile}

my $width = shift(@ARGV);

my $dna;
while (<>) {
    next if /^[#>]/;

    $dna .= $_;
}

$dna =~ s/[\s\d]//g;

# Initialize counts for motif positions
my %mot = map { $_ => [ (0) x $width ] } qw( A C G T );

# Initialize background counts
my %bg = map { $_ => 0 } qw( A C G T );

# Generate random start site in the sequence
# for motif to start from
my $ms = int(rand(length($dna)-$width));

# Within a motif, count the bases at the positions
for my $pos (0..length($dna)-1) {
    my $base = substr($dna, $pos, 1);
    if ($pos >= $ms && $pos < $ms + $width) {
        ++$mot{$base}[$pos-$ms]
            if exists($mot{$base});
    } else {
        ++$bg{$base}
           if exists($bg{$base});
    }
}

for my $base (qw( A C G T )) {
   print "$base @{$mot{$base}}\n";
}

print "\n";

for my $base (qw( A C G T )) {
   print "bg$base = $bg{$base}\n";
}