#!/usr/bin/perl -w
# Determining frequency of nucleotides, take 2

# Get the DNA sequence data
print "DNA sequence file: ";
$dna_filename = <STDIN>;
chomp $dna_filename;

# Does the file exist?
unless ( -e $dna_filename) {
    print "File \"$dna_filename\" doesn\'t seem to exist!!\n";
    exit;
}

# Can we access it?
unless ( open(DNAFILE, $dna_filename) ) {
    print "Cannot open file \"$dna_filename\"\n\n";
    exit;
}
@DNA = <DNAFILE>;
close DNAFILE;

$DNA = join( '', @DNA);
$DNA =~ s/\s//g;

# Initialize the counts.
$count_of_A = 0;
$count_of_C = 0;
$count_of_G = 0;
$count_of_T = 0;
$errors     = 0;

# In a loop, look at each base in turn, determine which of the
# four types of nucleotides it is, and increment the
# appropriate count.

for ( $position = 0 ; $position < length $DNA ; ++$position ) {

    $base = substr($DNA, $position, 1);

    if     ( $base eq 'A' ) {
        ++$count_of_A;
    } elsif ( $base eq 'C' ) {
        ++$count_of_C;
    } elsif ( $base eq 'G' ) {
        ++$count_of_G;
    } elsif ( $base eq 'T' ) {
        ++$count_of_T;
    } else {
        print Error - Unrecognized base:  $base\n";
        ++$errors;
    }
}

# print the results
print "A = $count_of_A\n";
print "C = $count_of_C\n";
print "G = $count_of_G\n";
print "T = $count_of_T\n";

if ($errors) {
	print "There were $errors unrecognized bases.\n";
}