--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/checkSnpEffCandidates.py	Mon Jun 25 16:12:55 2012 -0400
@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+import sys
+import optparse
+import csv
+import re
+
+def main():
+	parser = optparse.OptionParser()
+	parser.add_option('-s', '--snpeff_file', dest = 'snpeff_file', action = 'store', type = 'string', default = None, help = "Path to the snpEff file")
+	parser.add_option('-c', '--candidate_list', dest = 'candidate_list', action = 'store', type = 'string', default = None, help = "Two column tabular list of candidate Gene ID, Type")
+	parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")	
+	(options, args) = parser.parse_args()
+	
+	snpeff_file = options.snpeff_file
+	candidate_list = options.candidate_list
+
+	candidates = parse_candidate_list(candidate_list = candidate_list)
+	mark_snpeff_file(snpeff_file = snpeff_file, output = options.output, candidates = candidates)
+
+def skip_and_write_headers(writer = None, reader = None, i_file = None):
+	# count headers
+	comment = 0
+	while reader.next()[0].startswith('#'):
+		comment = comment + 1
+	
+	# skip and write headers
+	i_file.seek(0)
+	for i in range(0, comment):
+		row = reader.next()
+		writer.writerow(row)
+
+def parse_candidate_list(candidate_list = ""):
+	i_file = open(candidate_list, 'rU')
+	reader  = csv.reader(i_file, delimiter = '\t',)
+
+	candidates = {}
+	for row in reader:
+		gene_id = row[0]
+		gene_type = row[1]
+		candidates[gene_id] = gene_type
+
+	i_file.close()
+	
+	return candidates
+
+def mark_snpeff_file(snpeff_file = "", output = "", candidates = None):
+	i_file = open(snpeff_file, 'rU')
+	reader = csv.reader(i_file, delimiter = '\t')
+
+	o_file = open(output, 'wb')
+	writer = csv.writer(o_file, delimiter = '\t')
+
+	skip_and_write_headers(writer = writer, reader = reader, i_file = i_file)
+
+	for row in reader:
+		gene_id = row[9]
+		if gene_id in candidates:
+			gene_type = candidates[gene_id]
+			row.append(gene_type)
+		else:
+			row.append('')
+
+		writer.writerow(row)
+
+	o_file.close()
+	i_file.close()
+
+if __name__ == "__main__":
+    main()