Hello, I'm fixing a perl script for the lab I work at. This script used to work before our linux cluster underwent some update in 2017 (just for background). I'm workshopping each section of my script. I'm a perl novice, by the way! Everything before this block of code is working. The block of code below should open a file, find the $size of a chromosome from %chrsize, and iterate through a range of (0-$size). Currently, I've identified this strange issue: it will return a completely empty file. If I get rid of the if statement (where $piRNA{$chr}{$index} is set to zero), then the output file is still incorrect. It will return the $chr and $index formatted correctly, but will not print the last value. 

open OUT, ">", "$filename.counts";
foreach $chr (keys %chrsize){
    $size = $chrsize{$chr};  # chr, size, index work (print statements
+ show reasonable values)
    foreach $index (0..$size) {
       $piRNA{$chr}{$index}=0 if (!exists $piRNA{$chr}{$index});      
+ 
        print OUT "$chr\t$index\t$piRNA{$chr}{$index}\n";
     }
}

[download]

If I use an if-elsif statement, it still won't work. The only way I've gotten viable results is to specify that the script print to OUT only if $piRNA{$chr}{$index} exists. Can't I simply delete everything under the second foreach statement except for the "print OUT" statement, and wouldn't Perl automatically set "non-existent" keys to zero/undefined? 

open OUT, ">", "$filename.counts";
foreach $chr (keys %chrsize){
    $size = $chrsize{$chr};  # chr, size, index work (print statements
+ show reasonable values)
    foreach $index (0..$size) {
        if (exists $piRNA{$chr}{$index}) {
           print OUT "$chr\t$index\t$piRNA{$chr}{$index}\n";
        }
     }
}

[download]

I'd really appreciate any help or guidance, because my brain is fried.

In reply to If Condition causes totally blank Output File/Issue in Writing to Output by hghosh

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