G'day ila14,

Welcome to the monastery.

My biggest problem with this is determining the structure of the multidimensional hash you're trying to create.

Your description, "I would like to hash: % hash1 = Column1 => Column 2. %hash2 = %hash1 => Column3. %hash3 = %hash2 => Column 4.", conveys no real meaning. Your code is not helpful either: given you've stated "the syntax is not correct", this isn't too surprising.

From the code you've posted, I suspect you'd benefit from reading "perlintro -- a brief introduction and overview of Perl".

For information on data structures, I suggest you read "perldsc - Perl Data Structures Cookbook"; paying particular attention to the "HASHES OF HASHES" section.

The actual code you need may be as simple as this:

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

use constant {
    ID      => 0,
    SYMBOL  => 1,
    GO_ID   => 5,
    GO_NAME => 6,
};

my $file = './pm_1076856.tsv';
my %go_hash;

open my $fh, '<', $file;

while (<$fh>) {
    next if $. == 1;
    my @cols = split /\t/;
    $go_hash{$cols[SYMBOL]}{$cols[ID]}{$cols[GO_ID]} = $cols[GO_NAME];
}

use Data::Dump;
dd \%go_hash;
[download]

The file pm_1076856.tsv contains the input data you posted. Here's the output after running my example script:

{
  Symbol1 => { H1SXX9 => { "GO:0015031" => "protein transport" } },
  Symbol2 => {
               H1SXZ5 => {
                 "GO:0003824" => "catalytic activity",
                 "GO:0008152" => "metabolic process",
                 "GO:0008728" => "GTP diphosphokinase activity",
                 "GO:0015969" => "guanosine tetraphosphate metabolic p
+rocess",
                 "GO:0016301" => "kinase activity",
                 "GO:0016310" => "phosphorylation",
                 "GO:0016597" => "amino acid binding",
                 "GO:0016740" => "transferase activity",
               },
             },
  Symbol3 => {
               H1SXZ8 => {
                 "GO:0006812" => "cation transport",
                 "GO:0008324" => "cation transmembrane transporter act
+ivity",
                 "GO:0030001" => "metal ion transport",
                 "GO:0046872" => "metal ion binding",
                 "GO:0055085" => "transmembrane transport",
               },
             },
  Symbol4 => {
               H1SY02 => {
                 "GO:0006810" => "transport",
                 "GO:0008565" => "protein transporter activity",
                 "GO:0015031" => "protein transport",
               },
             },
  Symbol5 => {
               H1SY06 => {
                 "GO:0004129" => "cytochrome-c oxidase activity",
                 "GO:0005506" => "iron ion binding",
               },
             },
}
[download]

If that's close to what you want, try changing the hash depth and @cols indices to get whatever you require.

If that's completely different from what you're after, and you still can't work out what code you need, reduce your example data to a more manageable size for demonstration purposes (maybe half a dozen records) and post the actual data structure you require (something along the lines of my posted output would be preferable).

Also take a look at the guidelines in "How do I post a question effectively?" for hints and tips on what you can do to help us to help you.

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