To make sure that the lines with "NA" are not used simply change:

Code:

foreach $row (@data) {
        next unless $row =~ /^\d/;
        @dataline = split('\s',$row);
        next unless $dataline[87] =~ /$dataline[88]/i;
        print $dataline[0] . "\t" . $dataline[5] . "\t" . $dataline[87] . "\n";
}

to this

Code:

foreach $row (@data) {
        next unless $row =~ /^\d/;
        @dataline = split('\s',$row);
        next unless $dataline[87] ne "NA";
        next unless $dataline[87] =~ /$dataline[88]/i;
        print $dataline[0] . "\t" . $dataline[5] . "\t" . $dataline[87] . "\n";
}

As to the second problem, I am not sure I understand...


You say "attach" this code to the end of what we have already written. How are you "attaching" it?

Are you copying and pasting?
If so, are you removing the perl "shabang" at the top?
Are you simply calling this script from inside the other script at the end?
Can you verify that the file you are opening has the expected data?
Are you getting error, or no results at all?

---------- Post updated at 09:36 PM ---------- Previous update was at 08:54 PM ----------

After looking at the code you want to attach, I see some problems...

You should always have the following at the top of your code:

Code:

use strict;
use warnings;

This way you will get warnings and errors if the code is flawed.
I see that you do not properly initialize your variables, and these lines above would have immediately shown you that as well.

You will want something like this:

Code:

my 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
my dna = <DNAFILE>;
#close now read file
my lose DNAFILE;
#turn array into single string
my $dna = join('', @dna);
#get rid of blank spaces
my 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;

Then there are 2 lines above that I am not sure what you are trying to do with them...

Code:

#turn array into single string
$dna = join('', @dna);
#get rid of blank spaces
@dna =~ s/\s//g;

First naming the variable the same as the array (@dna vs $dna) is not a god idea.
Keep in mind that to access the "@data" array you write "$data[x]" (where x = index number of item).

Example:

Code:

#!/usr/bin/perl
use strict;
use warnings;

my @arr = qw(one two three);
print $arr[2] . "\n";

At the very least it is confusing. Then, you proceed to join the array to the string as one long string and remove spaces so you end up with:

Code:

onetwothree

and finally, you never actually USE "$dna", you only call "@dna" later.


Beyond that the code looks good, the foreach with the if/elsif/else block looks good.