--- a/gene_identification.py	Mon Mar 30 07:58:36 2015 -0400
+++ b/gene_identification.py	Wed Apr 01 05:09:59 2015 -0400
@@ -5,7 +5,7 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument("--input", help="The 1_Summary file from an IMGT zip file")
-parser.add_argument("--output", help="The annotated summary output file")
+parser.add_argument("--output", help="The annotated output file to be merged back with the summary file")
 
 args = parser.parse_args()
 
@@ -112,16 +112,17 @@
 		currentIDHits = hits[ID]
 		seq = dic[ID]
 		lastindex = 0
-		start = [0] * len(seq)
+		start_zero = len(searchstrings[key]) #allows the reference sequence to start before search sequence (start_locations of < 0)
+		start = [0] * (len(seq) + start_zero)
 		for i, regexp in enumerate(regularexpressions): #for every regular expression
 			relativeStartLocation = lastindex - (chunklength / 2) * i
-			if relativeStartLocation < 0 or relativeStartLocation >= len(seq):
+			if relativeStartLocation >= len(seq):
 				break
 			regex, hasVar = regexp
 			matches = regex.finditer(seq[lastindex:])
 			for match in matches: #for every match with the current regex, only uses the first hit
 				lastindex += match.start()
-				start[relativeStartLocation] += 1
+				start[relativeStartLocation + start_zero] += 1
 				if hasVar: #if the regex has a variable nt in it
 					chunkstart = chunklength / 2 * i #where in the reference does this chunk start
 					chunkend = chunklength / 2 * i + chunklength #where in the reference does this chunk end
@@ -140,7 +141,7 @@
 				continue
 			#print "found ", regex.pattern , "at", lastindex, "adding one to", (lastindex - chunklength / 2 * i), "to the start array of", ID, "gene", key, "it's now:", start[lastindex - chunklength / 2 * i]
 			currentIDHits[key + "_hits"] += 1
-		start_location[ID + "_" + key] = str([(removeAndReturnMaxIndex(start) + 1) for x in range(5) if len(start) > 0 and max(start) > 1])
+		start_location[ID + "_" + key] = str([(removeAndReturnMaxIndex(start) + 1 - start_zero) for x in range(5) if len(start) > 0 and max(start) > 1])
 		#start_location[ID + "_" + key] = str(start.index(max(start)))
 
 
@@ -161,7 +162,7 @@
 		for line in f:
 			total += 1
 			if first:
-				o.write(line.rstrip() + "\tbest_match\tnt_hit_percentage\tchunk_hit_percentage\tstart_locations\n")
+				o.write("Sequence ID\tbest_match\tnt_hit_percentage\tchunk_hit_percentage\tstart_locations\n")
 				first = False
 				continue
 			linesplt = line.split("\t")
@@ -169,6 +170,7 @@
 				pass
 			ID = linesplt[1]
 			currentIDHits = hits[ID]
+			print currentIDHits
 			possibleca = float(len(compiledregex["ca"]))
 			possiblecg = float(len(compiledregex["cg"]))
 			possiblecm = float(len(compiledregex["cm"]))
@@ -179,24 +181,24 @@
 				ca1hits = currentIDHits["ca1"]
 				ca2hits = currentIDHits["ca2"]
 				if ca1hits >= ca2hits:
-					o.write(line.rstrip() + "\tca1\t" + str(int(ca1hits / varsInCA * 100)) + "\t" + str(int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
+					o.write(ID + "\tca1\t" + str(int(ca1hits / varsInCA * 100)) + "\t" + str(int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
 				else:
-					o.write(line.rstrip() + "\tca2\t" + str(int(ca2hits / varsInCA * 100)) + "\t" + str(int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
+					o.write(ID + "\tca2\t" + str(int(ca2hits / varsInCA * 100)) + "\t" + str(int(cahits / possibleca * 100)) + "\t" + start_location[ID + "_ca"] + "\n")
 			elif cghits >= cahits and cghits >= cmhits: #its a cg gene
 				cg1hits = currentIDHits["cg1"]
 				cg2hits = currentIDHits["cg2"]
 				cg3hits = currentIDHits["cg3"]
 				cg4hits = currentIDHits["cg4"]
 				if cg1hits >= cg2hits and cg1hits >= cg3hits and cg1hits >= cg4hits: #cg1 gene
-					o.write(line.rstrip() + "\tcg1\t" + str(int(cg1hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tcg1\t" + str(int(cg1hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 				elif cg2hits >= cg1hits and cg2hits >= cg3hits and cg2hits >= cg4hits: #cg2 gene
-					o.write(line.rstrip() + "\tcg2\t" + str(int(cg2hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tcg2\t" + str(int(cg2hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 				elif cg3hits >= cg1hits and cg3hits >= cg2hits and cg3hits >= cg4hits: #cg3 gene
-					o.write(line.rstrip() + "\tcg3\t" + str(int(cg3hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tcg3\t" + str(int(cg3hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 				else: #cg4 gene
-					o.write(line.rstrip() + "\tcg4\t" + str(int(cg4hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+					o.write(ID + "\tcg4\t" + str(int(cg4hits / varsInCG * 100)) + "\t" + str(int(cghits / possiblecg * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 			else: #its a cm gene
-				o.write(line.rstrip() + "\tcm\t0\t" + str(int(cmhits / possiblecm * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
+				o.write(ID + "\tcm\t0\t" + str(int(cmhits / possiblecm * 100)) + "\t" + start_location[ID + "_cg"] + "\n")
 			seq_write_count += 1
 
 print "Time: %i" % (int(time.time() * 1000) - starttime)