comparison mutation_analysis.py @ 104:603a10976e9c draft

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103:e21cbe15381f

		IDlist += [ID]

AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] else 0)[4]) + 1)  # [4] is the position of the AA mutation, None if silent

AA_mutation = [0] * AALength
AA_mutation_empty = AA_mutation[:]

aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
with open(aa_mutations_by_id_file, 'w') as o:
	for ID in mutationListByID.keys():
		AA_mutation_for_ID = AA_mutation_empty[:]
		for mutation in mutationListByID[ID]:
			if mutation[4]:
				AA_mutation[int(mutation[4])] += 1
				AA_mutation_for_ID[int(mutation[4])] += 1
		o.write(ID + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")



#absent AA stuff

aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt"
with open(aa_mutations_file, 'w') as o:
	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n")
	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")

if linecount == 0:
	print "No data, exiting"
	with open(outfile, 'w') as o:

104:603a10976e9c

		IDlist += [ID]

AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] else 0)[4]) + 1)  # [4] is the position of the AA mutation, None if silent

AA_mutation = [0] * AALength
AA_mutation_dic = {"ca": AA_mutation[:], "cg": AA_mutation[:], "cm": AA_mutation[:], "un": AA_mutation[:]}
AA_mutation_empty = AA_mutation[:]

aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
with open(aa_mutations_by_id_file, 'w') as o:
	for ID in mutationListByID.keys():
		AA_mutation_for_ID = AA_mutation_empty[:]
		for mutation in mutationListByID[ID]:
			if mutation[4]:
				AA_mutation_position = int(mutation[4])
				AA_mutation[AA_mutation_position] += 1
				AA_mutation_for_ID[AA_mutation_position] += 1
				clss = genedic[ID][:2]
				AA_mutation_dic[clss][AA_mutation_position] += 1
		o.write(ID + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")



#absent AA stuff

aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt"
with open(aa_mutations_file, 'w') as o:
	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n")
	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")


aa_mutations_file_ca = outfile[:outfile.rindex("/")] + "/aa_mutations_ca.txt"
with open(aa_mutations_file_ca, 'w') as o:
	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["ca"][1:]]) + "\n")
	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")


aa_mutations_file_cg = outfile[:outfile.rindex("/")] + "/aa_mutations_cg.txt"
with open(aa_mutations_file_cg, 'w') as o:
	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n")
	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")


aa_mutations_file_cm = outfile[:outfile.rindex("/")] + "/aa_mutations_cm.txt"
with open(aa_mutations_file_cm, 'w') as o:
	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n")
	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")

if linecount == 0:
	print "No data, exiting"
	with open(outfile, 'w') as o: