Hello Perl Monks,

I am a novice and would be grateful for your help. I tried to write a piece of code to compare two files which look like

File 1

['CHROM', 'POS', 'REF', 'ALT', 'LIST', 'SAMPLE_1A', 'SAMPLE_2A', 'SAMP
+LE_3A']
['M, '16', 'T', 'C', 'C', 'REF', 'C', 'REF']
['M', '381', 'T', 'A', 'A', T', 'REF', 'REF']
['M', '529', 'A', 'G', 'G', 'REF', 'G', 'REF']
[download]

File 2

and

['CHROM', 'POS', 'REF', 'ALT', 'LIST', 'SAMPLE_1B', 'SAMPLE_2B', 'SAMP
+LE_3B']
['M', '16', 'T', 'C', 'C', 'C', 'REF', 'REF']
['M', '381', 'T', 'A', 'A', 'A', 'REF', 'REF']
['M', '528', 'A', 'G', 'G', 'REF', 'REF', 'REF']
[download]

I am trying to write a code which prints out file 1 again but if the sample value is not 'REF', looks up file 2. If the corresponding file 2 value is 'REF' then print the original value appearing in file 1. If the corresponding value in file 1 is not 'REF' then print the value we find in file 2. I also wish to ignore positions in file 2 not present in file 1. Using the examples above, my output for the first two rows should look like

['CHROM', 'POS', 'REF', 'ALT', 'LIST', 'SAMPLE_1A', 'SAMPLE_2A', 'SAMP
+LE_3A']
['M, '16', 'T', 'C', 'C', 'REF', 'C', 'REF']
['M', '381', 'T', 'A', 'A', 'A', 'REF', 'REF']
[download]

The code I have written so far is:

#!/usr/bin/local/perl

use strict;
use warnings;

my %HashRef = ();
my $File1 = 'blah.txt;
my $File2 = 'moreblah.txt';
my $outfile = 'blank.txt';

open FILE2, "< $File2" or die "could not open tumour file...\n";
open FILE1, "< $File1" or die "could not open host file...\n";
open( my $out_fh, '>', $outfile ) or die "$!";

while (my $cols = <FILE2>
{
    chomp $cols;
        my @values = split ',', $cols;
    for my $i(5..$#values)
        {
            push( @{$HashRef{ $values[2] }}, $values[$i]);
        }

}

while (my $cols = <FILE1>)
{
    chomp $cols;
    my @values =  split ',', $cols;
    my @newarray = ($values[0], $values[1], $values[2], $values[3], $v
+alues[
4]);
     for my $j(5..$#values)
    {
        if($values[$j] =~ m/'REF'/)
        {
        push(@newarray, $values[$j]);
        }
        elsif( $HashRef{ $values[$j]} =~ m/'REF'/)
        {
        push(@newarray, $values[$j]);
        }
        else
        {
            push(@newarray, " REF ");
        }
    }
    say $out_fh @newarray;
}
close $out_fh;
close file1;
close file2;
[download]

I keep getting the error "Use of uninitialized value within %HashRef in pattern match (m//) at test.pl line 45, <FILE1> line 27". I tried storing the columns I wanted from file 2 in a hash in order to look them up but it just doesn't seem to be working. I have tried everything I can think of but at this stage I am just running into a brick wall. Please help! Any and all suggestions/corrections/criticisms are welcome!

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.