Can I ask if I could also take a look at how you get the average of the ratio values as well?

Sure, here it is both makeRatioAvg and makeFinal 

    my $avgRatio = makeRatioAvg ( $ratio_ref );
    my $final    = makeFinal( $avgRatio ); 
    dd( { avgRatio => $avgRatio }, { final => $final } );


sub makeRatioAvg {
    print "makeRatioAvg \n";
    my( $ratio )  = @_;
    my $rows      = $#$ratio;
    my $columns   = $#{ $ratio->[0] };
    my $half_rows = $rows / 2;
    my $halff     = int( 1 + $half_rows );    ## eew
    my @avg;

    for my $tre ( 0 .. $columns ) {
        for my $tri ( 0 .. $columns ) {
            my $avg = 0;
            for my $six ( 0 .. $half_rows ) {
                my $val = $ratio->[$six][$tri][$tre];
                $avg += $val;
                print " + $val ";
            }
            $avg = $avg / $halff;
            print " == $avg \n";
            push @avg, $avg;
        }
    }
    for my $tre ( 0 .. $columns ) {
        for my $tri ( 0 .. $columns ) {
            my $avg = 0;
            for my $six ( $halff .. $rows ) {
                my $val = $ratio->[$six][$tri][$tre];
                $avg += $val;
                print " + $val ";
            }

#~             $avg = $avg / 3;
            $avg = $avg / $halff;
            print " == $avg \n";
            push @avg, $avg;
        }
    }

    return \@avg;
} ## end sub makeRatioAvg


sub makeFinal {
    my( $avgRatio ) = @_;
    my @first = @{$avgRatio}[ 0 .. ($#$avgRatio/2) ];
    my @second = @{$avgRatio}[ (1+($#$avgRatio/2) ) .. $#$avgRatio ];
    my @final = map { [ $first[$_] ] , [ $second[$_] ] } 0 .. $#first;
    return \@final;
}

[download]

As you might guess, makeRatioAvg and makeFinal is still me following closely the pencil and paper moves -- didn't want to get lost :) Now I have reference program with reference test data, so if I get ambitious and try to combine makeRatioAvg+makeFinal I will notice easily when I make mistake :)

Another question, when splitting the data (by tab since its tab delimited file), it will be split according to columns right (downwards). Is it possible to split by rows (horizontal)? Will that be easier for this kind of ratio thing or it doesn't make a difference?

I'm not quite sure what you mean, but I doubt it makes much of a difference, here is why

rows are lines ... each lines consists of tab seperated values (columns of a row) , so you're already doing what is possible in the most straight forward way

the only issue I saw with your code is you had "while while" loop, where the outer while was used just for the header ... I wrote that as 

sub spankTheMonkey {
    my( $infh ) = @_;
    my @full_data;
    my $header = readline $infh;
    if( $header =~ /\d+/ ) {    ## in case there is no header
        push @full_data, [ split ' ', $header ];
    }
    push @full_data, [split] while( <$infh> );
    return \@full_data;
} ## end sub spankTheMonkey

[download]

It was called from DoWorkOriginal 

sub DoWorkOriginal {
    my( $firstinput, $secondinput, $inFile, $outFile ) = @_;
    use autodie qw/ open close /;
    open my $curInfile, '<:raw', $inFile;     ## or die by autodie
    open my $OUT1,      '>:raw', $outFile;    ## or die by autodie

    my $full_data = spankTheMonkey( $curInfile );
    monkeyBusiness( $firstinput, $secondinput, $OUT1, $full_data );
    
    close $curInfile;
    close $OUT1;
} ## end sub DoWorkOriginal

[download]

Where sub monkeyBusiness is the foreach loops from your code which I didn't understand

The general strategy when I don't understand why/how something works, before I can begin to debug/improve, is to isolate/sequester everything into subroutines, and make sure it produces same output as original

In reply to Re^19: How to store the output from foreach loop into variable/array without printing? by Anonymous Monk
in thread How to store the output from foreach loop into variable/array without printing? by hellohello1

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.