use warnings;
use strict;
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you would have gotten these error messages:

Bareword "DUMMYHUGO" not allowed while "strict subs" in use ...
Bareword "DUMMY_GENEFILE" not allowed while "strict subs" in use...
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This would have lead you to suspect some kind of problem with these lines of code:

@hugo = DUMMYHUGO;
    @genes = DUMMY_GENEFILE;
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It is not really clear what you are trying to do, but if you are trying to match names in the genes file to any name on any line of the hugo file, the following code might be a step in the right direction. Please note that this is not an attempt at a complete solution:

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

my @hugos;
open my $DUMMYHUGO, '<', 'DummyHugo.txt' or die "cannot open file cont
+aining HUGO IDs: $!\n";
while (<$DUMMYHUGO>) {
    my @hugo = split;
    push @hugos, [@hugo];
}
close $DUMMYHUGO;

my $outfile = 'HUGO_dummyResults.txt';
open my $OUT,            '>', $outfile          or die "cannot create 
+the output file: $!\n";
open my $DUMMY_GENEFILE, '<', 'DummyGenes.txt'  or die "cannot open fi
+le containing genes: $!\n";
while (<$DUMMY_GENEFILE>) {
    my @genes = split;
    for my $href (@hugos) {
        my @hugo = @{$href};
        for (my $i = 5; $i < 9; $i++) {
            if ($genes[2] eq $hugo[$i]) {
                print $OUT "$genes[0]\t$genes[1]\t$genes[2]\t$genes[3]
+\t$hugo[1]\n";
            }
        }
    }
}
close $DUMMY_GENEFILE;
close $OUT;
exit;
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The output file will then contain:

ID1    Id2    Katie    Path    KJRJ
ID1a    Id2a    Dave    Path    DJL
ID1b    Id2b    Kean    Path    PKKJ
ID1c    Id2c    Paul    Path    PKKJ
ID1d    Id2d    Sandra    Path    SKJ
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This code reads the hugo file into an array of arrays, @hugos, then reads the genes file one line at a time and checks if the gene name matches any name on any line in the hugo file.

I hope this helps.

Thank you for your quick response, that is exactly the output I would like to see.
I will have a play and see what happens.

Dear toolic,
This script works beautifully on my dummy data.

When I run it using my real files I get an error message that repeats itself line after line until I stop it.

Use of uninitialized value in string eq at HUGOID_extract.pl line 50, <$GENEFILE> line 1.


Read more... (2 kB)

The code I posted, as I mentioned, was not a complete solution. The code assumed that every line in the genes file would have at least 3 columns and that every line in the hugo file would have at least 9 columns, since this is what your dummy input sample files had.

If your actual files have fewer columns, then you might get those warnings.

If your actual files have blank lines, then you might get those warnings.

It is impossible for me to know the structure of your input files without seeing more (small) examples. My guess is that you now need to check the format of your input. For example, you could check how many columns are in each line of the genes file by checking how many elements are in the array:

my $cols = scalar @genes;
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Are you sure the code is looping infinitely? I could believe that the code would take a long time to run if your input files are really big (1 million lines, many columns per line).

No need to apologize; I think you code is very well formated. Kudos on a well stated and complete question also. Why don't you sign in so you can collect XP and gain fame and fortune? Well the fortune part is probably a stretch but seriously, Get a login if you don't have one and sign in, the site could use your participation.

Ooh, aren't you all terribly nice. I was terrified to post here, let alone register! I think I will because over the course of my PhD I will have to become much more adept at perl and I'm sure I will be baying with frustration on more than one occasion. Thanks again.