my $resultFile= "C://Users/kullaniciadi/Desktop/plasmodium/results.txt
+";
open (OUT, ">>$resultFile") or die ("Cannot open $resultFile");

open(geneREAD, $plasData) or die ("Cannot open $plasData");
my ($geneName, $line2, $epitope, $epiSeq, $locBeg, $locEnd);
my $ctr;

while($line2=<geneREAD>)
{
    $ctr=0;
    chomp($line2);
    if($line2=~ m/^Gene:\s*(.*)/)
    {
        $geneName= $1;
        if(grep(/^$geneName$/, @geneArr))
        {
            while(substr($line2, 0 , 3) ne "---")
            {
                $line2=<geneREAD>;
                chomp($line2);
                if($line2=~ m/(\d+)\s+([A-Z]+)\s+(\d+)-(\d+)/)
                {
                    $epitope= $1;
                    $epiSeq= $2;
                    $locBeg=$3;
                    $locEnd=$4;
                    
                    foreach $snpID(@ {$snpHash{$geneName}})#call some 
+values parsed earlier in the code from an array of hashes and compare
+ them with locBeg & locEnd
                    {
                        
                        if($locBeg <= $HoProPos{$snpID} && $HoProPos{$
+snpID} <= $locEnd)
                        {
                            if($ctr== 0)#this $ctr thing is used to pr
+int out gene's name only once in the output file
                            {print OUT "Gene: $geneName\n";}
                            print OUT "SNP $snpID found in epitope $ep
+itope at protein position $HoProPos{$snpID}\n";
                            $ctr=1;
                        }
                    }
                }
            }
        }
    }
}
[download]

Well, this is the part with the file handle you are mentioning. I only changed *s to +s in the inner if as I told you. I somehow do not believe that the warnings thrown pointing to dashed lines (in the .* version of the code) of the doc has anything to do with this filehandle, since it looks pretty simple and easy.

Thank you for your help. Looks much more better with new declarations and changes. Hopefully I'll get used to it over time.