Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.py @ 66:43a1aa648537 draft

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author davidvanzessen
date Thu, 07 Dec 2017 03:44:38 -0500
parents 8728284105ee
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65:dc06e94bc1e3 66:43a1aa648537
247 247
248 AA_mutation = [0] * AALength 248 AA_mutation = [0] * AALength
249 AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]} 249 AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
250 AA_mutation_empty = AA_mutation[:] 250 AA_mutation_empty = AA_mutation[:]
251 251
252 print "AALength:", AALength
252 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt" 253 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
253 with open(aa_mutations_by_id_file, 'w') as o: 254 with open(aa_mutations_by_id_file, 'w') as o:
254 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n") 255 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
255 for ID in mutationListByID.keys(): 256 for ID in mutationListByID.keys():
256 AA_mutation_for_ID = AA_mutation_empty[:] 257 AA_mutation_for_ID = AA_mutation_empty[:]
257 for mutation in mutationListByID[ID]: 258 for mutation in mutationListByID[ID]:
258 if mutation[4]: 259 if mutation[4] and mutation[5] != ";":
259 AA_mutation_position = int(mutation[4]) 260 AA_mutation_position = int(mutation[4])
260 AA_mutation[AA_mutation_position] += 1 261 try:
261 AA_mutation_for_ID[AA_mutation_position] += 1 262 AA_mutation[AA_mutation_position] += 1
263 AA_mutation_for_ID[AA_mutation_position] += 1
264 except Exception as e:
265 print e
266 print mutation
267 sys.exit()
262 clss = genedic[ID][:3] 268 clss = genedic[ID][:3]
263 AA_mutation_dic[clss][AA_mutation_position] += 1 269 AA_mutation_dic[clss][AA_mutation_position] += 1
264 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n") 270 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
265 271
266 272