#!/usr/bin/perl -w

print "Please type the filename of the Chromosome: ";

$chromosomefilename = <STDIN>;

chomp $chromosomefilename;

unless ( open(CHROMOSOMEFILE, $chromosomefilename) ) {

print "Cannot open file \"$chromosomefilename\"\n\n";

exit;

}

@chromosome = <CHROMOSOMEFILE>;

close CHROMOSOMEFILE;

$chromosome = join( '', @chromosome);

$chromosome =~ s/\s//g;

do {

print "Enter the Recognition Sequence to search for: ";

$recognitionsequence = <STDIN>;

chomp $recognitionsequence;

my @words = qw ($chromosomefilename);

my $count = grep /$recognitionsequence/, @words;

print "\$count = $count\n";

} until ( $recognitionsequence =~ /^\s*$/ );

exit;