--- a/mutation_analysis.py	Wed May 04 04:28:02 2016 -0400
+++ b/mutation_analysis.py	Wed May 04 08:40:31 2016 -0400
@@ -7,7 +7,7 @@
 parser.add_argument("--input",
 					help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation")
 parser.add_argument("--genes", help="The genes available in the 'best_match' column")
-parser.add_argument("--includefr1", help="The genes available in the 'best_match' column")
+parser.add_argument("--includefr1", help="Should the mutation/nucleotides in the FR1 region be included?")
 parser.add_argument("--output", help="Output file")
 
 args = parser.parse_args()
@@ -57,6 +57,7 @@
 		linesplt = line.split("\t")
 		ID = linesplt[IDIndex]
 		genedic[ID] = linesplt[best_matchIndex]
+		print line
 		try:
 			mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[fr1Index].split("|") if x] if include_fr1 else []
 			mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr1Index].split("|") if x]