# HG changeset patch
# User davidvanzessen
# Date 1512636278 18000
# Node ID 43a1aa648537827ab031b667d2ade4ec8b4fc7a0
# Parent  dc06e94bc1e34b4ef32df6872d6345c09bf83355
Uploaded

diff -r dc06e94bc1e3 -r 43a1aa648537 shm_csr.py
--- a/shm_csr.py	Wed Dec 06 09:55:37 2017 -0500
+++ b/shm_csr.py	Thu Dec 07 03:44:38 2017 -0500
@@ -249,16 +249,22 @@
 	AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
 	AA_mutation_empty = AA_mutation[:]
 
+	print "AALength:", AALength
 	aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
 	with open(aa_mutations_by_id_file, 'w') as o:
 		o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
 		for ID in mutationListByID.keys():
 			AA_mutation_for_ID = AA_mutation_empty[:]
 			for mutation in mutationListByID[ID]:
-				if mutation[4]:
+				if mutation[4] and mutation[5] != ";":
 					AA_mutation_position = int(mutation[4])
-					AA_mutation[AA_mutation_position] += 1
-					AA_mutation_for_ID[AA_mutation_position] += 1
+					try:
+						AA_mutation[AA_mutation_position] += 1
+						AA_mutation_for_ID[AA_mutation_position] += 1
+					except Exception as e:
+						print e
+						print mutation
+						sys.exit()
 					clss = genedic[ID][:3]
 					AA_mutation_dic[clss][AA_mutation_position] += 1
 			o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")