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 print out gene's name only once in the output file
							{print OUT "Gene: $geneName\n";}
							print OUT "SNP $snpID found in epitope $epitope at protein position $HoProPos{$snpID}\n";
							$ctr=1;
						}
					}
				}
			}
		}
	}
}