#!/usr/bin/perl
#
use strict;
use warnings;
my (@data, $row, @dataline);
open(FILE1,"<","UDP3866.pseudo-vs.large.txt") or die $!; @data = <FILE1>; close(FILE1);
foreach $row (@data) {
        next unless $row =~ /^\d/;
        @dataline = split(/\s+/,$row);
        next unless $dataline[9] ne "NA";
        next unless $dataline[9] =~ /$dataline[6]/i;
        print $dataline[0] . "\t" . $dataline[1] . "\t" . $dataline[6] . "\t" .  $dataline[7] . "\t" . $dataline [9] .  "\n";
}
my $outputfile = "COUNTBASE";
unless (open(COUNTBASE, ">$outputfile")) {print "cant open file\n\n";
exit;}
print COUNTBASE "$dataline[7]";
close (COUNTBASE);
my $dnafile = <COUNTBASE>;
#Remove the newline from the dna file name
chomp $dnafile;
#Open this file or exit
unless (open(COUNTBASE, $dnafile)){
         print  "can't open file \"$dnafile\"\n\n";
        exit;
}
#store dna information
my @dna = <COUNTBASE>;
#close now read file
close COUNTBASE;
#turn array into single string
my $dna = join('', @dna);
#get rid of blank spaces
$dna =~ s/\s//g;
#initialize mutation counts
my $countExonic = 0;
my $countIntergenic = 0;
my $countIntronic = 0;
my $countUpstream = 0;
my $countDownstream = 0;
my $countUTR5 = 0;
my $countUTR3 = 0;
my $countFrameshift = 0;
my $countNonsynonomous = 0;
my $countSyn = 0;
my $countStopgain = 0;
my $countStoploss = 0;
my $countSplicing = 0;
 
my $countErrors = 0;
#create loop to search for mutations
foreach (@dna) {
        if ( /exonic/ ) {
                ++$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;

 
readline() on closed filehandle COUNTBASE at 5drag.pl line 22.
Use of uninitialized value $dnafile in scalar chomp at 5drag.pl line 25.
Use of uninitialized value $dnafile in open at 5drag.pl line 28.
Use of uninitialized value $dnafile in concatenation (.) or string at 5drag.pl line 29.
can't open file ""