gsea.py

#!/usr/bin/env python
'''
@author: Jens Preussner <jens.preussner@mpi-bn.mpg.de>

This is a wrapper for Julia Bayers geneset enrichment analysis program.

Input:
sys.argv[1] - geneset dictionary, key=name of geneset, value=list of genes (strings)
sys.argv[2] - tab separated rank file, 1st col genes, 2nd col rank
sys.argv[3] - output base
'''

import sys
import enrichAnalysis
import json

try:
	with open(sys.argv[1]) as geneset_dict:
		genesets = json.load(geneset_dict)
except IOError as e:
	print("Unable to open file "+sys.argv[1]+". File might not exist or missing read permissions.")


ranks = []
try:
	with open(sys.argv[2]) as rank_file:
		for line in rank_file:
			ranks.append(line)
except IOError as e:
	print("Unable to open file "+sys.argv[2]+". File might not exist or missing read permissions.")

enrichAnalysis.main(mti_d = genesets, rank_l = ranks, s_path = sys.argv[3]+'-genesets_ranked.txt', h_path = sys.argv[3]+'-geneset_overlap.pdf', e_path = sys.argv[3], le_path = sys.argv[3]+'-geneset_genes.txt')