Dear Marshall, I do not know if you're interested in this code at all :) but let me clarify a little bit. Let me start with explaining what $HoProPos{$snpID} is.

$HoProPos is a hash as can be understood, which contains positions of snps(single nucleotide polymorphisms) in a protein structure. snpIDs are key values of this hash and since every snp ID is unique I thought it's a good way to hash them for fast and easy access to their locations in the proteins through their names. now, where do I get this data at all, its not in the above code? I get/parse this data from another inputfile somewhere earlier in the code which i thought posting would be unnecessary.

so, the thing I was trying to accomplish is basically. Parsing the first input file, storing snpIDs, in what genes (@geneArr) they are located at, and at what position of the that protein ($HoProPos{snpID}} (translated form of that gene) they are occurring.

Then I open another file (the file above, in the original post) which has information about genes and the epitopes they contain. And I check if the gene name exists in my @geneArr which contains genes with snps inside, if exists, I check the location of the corresponding snp to see whether if that snp is located somewhere in between the start or stop point of the epitope (($locBeg <= $HoProPos{$snpID} && $snploc <= $HoProPos{$snpID})).

As i said, the code works pretty fine right now. The only thing I could not understand as I said, when Perl threw warnings, the warnings were pointed to the lines with dashes. If I know a little bit programming the dashed lines never went into the if in which the comparison took place (before or after the substitution of .* with .+). So, I don't know why Perl pointed to those lines.

Thank you for your time.