Re^19: How to store the output from foreach loop into variable/array without printing?

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

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Re^20: How to store the output from foreach loop into variable/array without printing? by hellohello1 (Sexton) on Mar 21, 2014 at 08:38 UTC
Thank you :) I am a very slow learner, so it will take me quite a while for me to digest and reply you. Before that, I want to clarify something really noob: `my( $infh ) = @_;` [download] @_ refer to the whole dataset right? But if I want to only include data from column 4 onward to the end, I have to write a function to split the data and then take column 4 to end and put it into @_?	[reply] [d/l]
Re^21: How to store the output from foreach loop into variable/array without printing? by Anonymous Monk on Mar 21, 2014 at 08:54 UTC
@_ refer to the whole dataset right? Do a ctrl+f for spankTheMonkey to see what spankTheMonkey is being given (which args are passed) Then see perlvar#@_ Within a subroutine the array @_ contains the parameters passed to that subroutine. So, @_ is not "the whole dataset", there is no variable "the whole" of type "dataset" :) But if I want to only include data from column 4 onward to the end, I have to write a function to split the data and then take column 4 to end and put it into @_? Yes, you can modify spankTheMonkey to discard parts ... essentially turning it from readFullData into readColumnRange( $in_filehandle, 4 .. 10 ); perlintro#Arrays ought to help	[reply]
Re^22: How to store the output from foreach loop into variable/array without printing? by hellohello1 (Sexton) on Mar 24, 2014 at 01:41 UTC
ok! Thank you for the clarification! I'll get back to reading all these up. :)	[reply]
Re^22: How to store the output from foreach loop into variable/array without printing? by hellohello1 (Sexton) on Mar 25, 2014 at 09:22 UTC
Hi, ok. I actually continue using my code as I feel more familiarize with it but did accordingly to how you advise me and I can come out with the output I want: while(<CURINFILE>) { push @full_data , [split] while (<CURINFILE>); for $arr_ref1 (@full_data) { for $arr_ref2(@full_data) { $variable1 = ''; $variable2 = ''; for my $index1 (3..4) { $ratio1 = sprintf( "%.4f%s", $$arr_ref2[$index1]/$$arr_ref1 +[$index1],"\t"); $variable1 .= $ratio1; } for my $index2 (5..6) { $ratio2 = sprintf( "%.4f%s", $$arr_ref2[$index2]/$$arr_ref1 +[$index2],"\t"); $variable2 .= $ratio2; } #Calculate Average @arrayint1 = split (/\t/,$variable1); $avg1 = &average (\@arrayint1); #print OUT1 "\t$avg1"; @arrayint2 = split (/\t/,$variable2); $avg2 = &average (\@arrayint2); #print OUT1 "\t$avg2"; #Calculate SD @arrayint1 = split (/\t/,$variable1); $std1 = &stdev(\@arrayint1); #print OUT1 "\t$std1"; @arrayint2 = split (/\t/,$variable2); $std2 = &stdev(\@arrayint2); #print OUT1 "\t$std2"; #Calculate CV $cv1 = $std1/$avg1; $cv2 = $std2/$avg2; my $outputa = "$$arr_ref1[0]"; my $outputb = "$variable1\t$variable2\t"; my $outputc = "\t$avg1\t$avg2"; my $outputd = "\t$cv1\t$cv2"; ###### print everything out ##################### my $key = "$outputa"."$outputb". "$outputc"."outputd"; print OUT1 $key; print OUT1 "\n"; } } sub average{ my($data) = @_; if (not @$data) { die("Empty array\n"); } my $total = 0; foreach (@$data) { $total += $_; } my $average = $total / @$data; return $average; } sub stdev{ my($data) = @_; if(@$data == 1){ return 0; } my $average = &average($data); my $sqtotal = 0; foreach(@$data) { $sqtotal += ($average-$_) 2; } my $std = ($sqtotal / (@$data-1)) 0.5; return $std; } [download] so the output will be : `_OUTPUT_ M446T27 1 1 1 1 1 1 0 0 M446T27 1.75 2.66 1.80 2.16 2.20 1.98 0.29 0.12 M446T27 1.00 1.64 0.99 1.09 1.32 1.04 0.34 0.06 . .` [download] So far so good. Phew! Thanks to your guidance! :) My next question is, is it possible to actually filter the whole row based on the outputd(set condition)? (not sure if it should be put into a new thread?)	[reply] [d/l] [select]
Re^23: How to store the output from foreach loop into variable/array without printing? by Anonymous Monk on Mar 25, 2014 at 15:28 UTC