#!/usr/bin/perl
#Ask user for file that is to be read
print "please type name of file: ";
$dnafile = <>;
#Remove the newline from the dna file name
chomp $dnafile;
#Open the file or exit
unless (open(DNAFILE, $dnafile)){
         print  "can't open file \"$dnafile\"\n\n";
        exit;
}
#store dna information
@dna = <DNAFILE>;
#close now read file
close DNAFILE;
#turn array into single string
$dna = join('', @dna);
#get rid of blank spaces
$dna =~ s/\s//g;
#initialize mutation counts
$countExonic = 0;
$countIntergenic = 0;
$countIntronic = 0;
$countUpstream = 0;
$countDownstream = 0;
$countUTR5 = 0;
$countUTR3 = 0;
$countFrameshift = 0;
$countNonsynonomous = 0;
$countSyn = 0;
$countStopgain = 0;
$countStoploss = 0;
$countSplicing = 0;
$countErrors = 0;
#create loop to search for mutations
foreach (@dna) {
        if ( /exonic/ ) {
                ++$countExonic;
        } elsif ( /inter/ ){
                ++$countIntergenic;
        } elsif ( /intron/ ){
                ++$countIntronic;
        } elsif ( /upstream/ ){
                ++$countUpstream;
        } elsif ( /downstream/ ){
                ++$countDownstream;
        } elsif ( /UTR5/ ) {
                ++$countUTR5;
        } elsif ( /UTR3/ ){
                ++$countUTR3;
        } elsif ( /frame/ ){
                ++$countFrameshift;
        } elsif ( /nonsyn/ ){
                ++$countNonsynonomous;
        } elsif ( /syn/ ) {
                ++$countSyn;
        } elsif ( /gain/ ) {
                ++$countStopgain;
        } elsif ( /loss/ ) {
                ++$countStoploss;
        } elsif ( /splic/ ) {
                ++$countSplicing;
        } else  {++$countErrors;
        }
}
#print out results
print "Exonic Mutations = $countExonic\n\n";
print "Intergenic Mutations = $countIntergenic\n\n";
print "Intronic Mutations = $countIntronic\n\n";
print "Upstream Mutations = $countUpstream\n\n";
print "Downstream Mutations = $countDownstream\n\n";
print "UTR5 Mutations = $countUTR5\n\n";
print "UTR3 Mutations = $countUTR3\n\n";
print "Frameshift Mutations = $countFrameshift\n\n";
print "Nonsynonomous Mutations = $countNonsynonomous\n\n";
print "Sysnonomous Mutations = $countSyn\n\n";
print "Stop/Gain Mutations = $countStopgain\n\n";
print "Stop/Loss Mutations = $countStoploss\n\n";
print "Splicing Mutations = $countSplicing\n\n";
print "Others = $countErrors\n\n";
#exit the program
exit;