Are those lines empty or full of tab characters? Maybe the CytokineArrays.txt file ends by some 900 empty lines. Try to add 

 next unless /\S/;

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after the chomp; in the second loop.

Also, there is no difference between $var =~ /\S+/ and $var =~ /\S/. Except that the later will probably be quicker. Both return true whenever there is at least one non-whitespace-character anywhere in the $var. Same with the \d. Maybe you wanted $var =~ /^\S+$/. Which means ... make sure the $var contains only non-whitespace-characters and is not empty.

Update: fixed the typo noticed by jwkrahn. I meant \S+ and wrote \s+.

Jenda
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In reply to Re^3: Print function by Jenda
in thread Print function by de2425

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