#!/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;
}