my @content = (<FH>);

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;
use autodie ':all';

use Data::Dump;
use Text::CSV;

{
    my $source_file = 'pm_11116298_gene.txt';

    show_verbatim_input($source_file);
    process_without_2d_array($source_file);
    my $data_2d_ref = process_with_2d_array($source_file);
    # Do more processing with $data_2d_ref
}

sub process_without_2d_array {
    my ($file) = @_;

    print "\n\n+++++ WITHOUT INTERMEDIATE 2D ARRAY +++++\n";

    my @proteins;
    my %count_of = (just_mfs => {}, all_mf_elements => {});

    {
        open my $fh, '<', $file;
        { my $header_record_to_discard = <$fh>; }
        my $csv = Text::CSV::->new({sep => "\t"});

        print "\n*** Wanted Data Output ***\n";

        while (my $row = $csv->getline($fh)) {
            push @proteins, $row->[0];
            $count_of{just_mfs}{$row->[0]} = $#$row;
            $count_of{all_mf_elements}{$row->[0]}
                += scalar map split, @$row[1..$#$row];
            print join('; ', @$row), "\n";
        }
    }

    print "\n*** Wanted Row Counts (GUESS 1) ***\n";
    print "$_ : $count_of{just_mfs}{$_}\n" for @proteins;

    print "\n*** Wanted Row Counts (GUESS 2) ***\n";
    print "$_ : $count_of{all_mf_elements}{$_}\n" for @proteins;

    return;
}

sub process_with_2d_array {
    my ($file) = @_;

    print "\n\n+++++ WITH INTERMEDIATE 2D ARRAY +++++\n";

    my @data_2d;

    {
        open my $fh, '<', $file;
        { my $header_record_to_discard = <$fh>; }
        my $csv = Text::CSV::->new({sep => "\t"});

        while (my $row = $csv->getline($fh)) {
            push @data_2d, $row;
        }
    }

    print "\n*** 2D Array of Data ***\n";
    dd \@data_2d;

    print "\n*** Wanted Data Output ***\n";
    print join('; ', @$_), "\n" for @data_2d;

    print "\n*** Wanted Row Counts (GUESS 1) ***\n";
    print "$_->[0] : $#$_\n" for @data_2d;

    print "\n*** Wanted Row Counts (GUESS 2) ***\n";
    print "$_->[0] : ",
        scalar(map split, @$_[1..$#$_]), "\n" for @data_2d;

    return \@data_2d;
}

sub show_verbatim_input {
    my ($file) = @_;

    print "*** Input File ($file) ***\n",
          "        ('^I' = TAB; '\$' = NEWLINE)\n";
    system qw{cat -vet}, $file;

    return;
}

##</code><code>##

*** Input File (pm_11116298_gene.txt) ***
        ('^I' = TAB; '$' = NEWLINE)
ProteinName^IMF1^IMF2^IMF3$
GH1^IGrowth factor activity^IGrowth hormone receptor binding^IHormone activity$
POMC^IG protein-coupled receptor binding^IHormone activity^ISignaling receptor binding$
THRAP3^IATP binding Source^INuclear receptor transcription coactivator activity^IPhosphoprotein binding$


+++++ WITHOUT INTERMEDIATE 2D ARRAY +++++

*** Wanted Data Output ***
GH1; Growth factor activity; Growth hormone receptor binding; Hormone activity
POMC; G protein-coupled receptor binding; Hormone activity; Signaling receptor binding
THRAP3; ATP binding Source; Nuclear receptor transcription coactivator activity; Phosphoprotein binding

*** Wanted Row Counts (GUESS 1) ***
GH1 : 3
POMC : 3
THRAP3 : 3

*** Wanted Row Counts (GUESS 2) ***
GH1 : 9
POMC : 9
THRAP3 : 10


+++++ WITH INTERMEDIATE 2D ARRAY +++++

*** 2D Array of Data ***
[
  [
    "GH1",
    "Growth factor activity",
    "Growth hormone receptor binding",
    "Hormone activity",
  ],
  [
    "POMC",
    "G protein-coupled receptor binding",
    "Hormone activity",
    "Signaling receptor binding",
  ],
  [
    "THRAP3",
    "ATP binding Source",
    "Nuclear receptor transcription coactivator activity",
    "Phosphoprotein binding",
  ],
]

*** Wanted Data Output ***
GH1; Growth factor activity; Growth hormone receptor binding; Hormone activity
POMC; G protein-coupled receptor binding; Hormone activity; Signaling receptor binding
THRAP3; ATP binding Source; Nuclear receptor transcription coactivator activity; Phosphoprotein binding

*** Wanted Row Counts (GUESS 1) ***
GH1 : 3
POMC : 3
THRAP3 : 3

*** Wanted Row Counts (GUESS 2) ***
GH1 : 9
POMC : 9
THRAP3 : 10