Geneset=GO0035091	Size=77  	ES=0.525	NES=2.913	NominalP=0.000	
Geneset=GO0030163	Size=54  	ES=0.463	NES=2.248	NominalP=0.013	
Geneset=GO0007067	Size=44  	ES=0.484	NES=1.975	NominalP=0.018	
##</code><code>##

GO0046800	GO0046800	CD209	CD209L	CD209L1	CD209_HUMAN	CLC4M  
GO0032104	GO0032104	CART	CARTPT	CART_HUMAN	GHRL	GHRL_HUMAN
.........	..........	.....	......	..........	....	..........
.........	..........	.....	......	..........	....	..........
GO0035091	GO0035091	41_HUMAN	5NTD_HUMAN	9804	A-388D4.1	.....
##</code><code>##

rs10904494	NP_817124	17881
rs7906287	NP_817124	39800
rs4881551	41_HUMAN	21567
rs5416721	5NTD_HUMAN	0
.................... 	..............	....
##</code><code>##

Marker	         CHI2
rs3749375	11.7268615355335
rs10499549	10.4656064706897
rs5416721	9.85374546064131
##</code><code>##

Geneset		Genes		SNP/Marker	ES	NES		NominalP
GO0035091	41_HUMAN	rs4881551	....	.......	....
			5NTD_HUMAN	rs5416721	....	.......	....	
....................	....................	.................. 
##</code><code>##

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";
				
				}
	}
	}