open(OUTPUT, "<C:\\Documents and Settings\\shra1\\Desktop\\prj\\schneider_breast_copy_num_pathway_enrichment1.txt");
@output = <OUTPUT>;
close(OUTPUT);

open(GENESETS, "<C:\\Documents and Settings\\shra1\\Desktop\\prj\\human.gmt");
@geneSets = <GENESETS>;
close(GENESETS);
@NewgeneSet;
@genesInSet;


$i=0;
while($i < 10){
	@outputLineSplit = split(/\t/,$output[$i]);
	#print "$outputLineSplit[0] \n";
	
	$setName = $outputLineSplit[0];
	
	$equalLoc = index($setName, "=");
	$setName = substr($setName,$equalLoc+1,length($setName));
	#print "$setName\n";
	@genesInSet[$i]= $setName;
	$i++;
}

foreach $genesInSet(@genesInSet){
	print "$genesInSet\n";
		foreach $geneSets(@geneSets){
		if($geneSets=~m/$genesInSet/i){
		#print "$geneSets\n";
				
				}
	}
	}