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.

In reply to Re^2: Argument "" isn't numeric in numeric le (<=) by hotel
in thread Argument "" isn't numeric in numeric le (<=) by hotel

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.