Hi SilverWol,

choroba has corrected your errors and solved your issue, but I would suggest a slightly different approach based on the fact that the @hub array isn't really necessary: you can print out the data as soon as you've isolated the gene that needs to be printed. Something like this (untested):

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

open my $HUBFILE, '<', '1048_undefined.tsv' or die $!;
open my $OUT, '>', 'hubs.txt' or die $!;
while (my $line = <$HUBFILE>) {
    my $gene = $1 if $line =~ /\d \t (\w+) \t/x;
    print $OUT, $gene, "\n";
}
close $_ for ($HUBFILE, $OUT);
[download]

The code is slightly shorter and probably slightly faster, but the main advantage is that this will work even with a huge input file, while the solution with an intermediate array might fail if the array grows to big for your available memory.

Update: corrected the name of the addressee at the top of this post (wrong copy and paste, I guess). Thanks to choroba for pointing it out the error.

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