comparison shm_csr.py @ 48:c5295dd10dfc draft

Uploaded

47:64711f461c8e

	#tandem mutation stuff
	tandem_frequency = defaultdict(int)
	mutation_frequency = defaultdict(int)

	tandem_file = os.path.join(os.path.dirname(outfile), "tandems_by_id.txt")
	with open(tandem_file, 'w') as o:
		highest_tandem_length = 0

		o.write("Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n")

				if highest_tandem_length < len(tandem_muts):
					highest_tandem_length = len(tandem_muts)

			region_length = fr1LengthDict[ID] + cdr1LengthDic[ID] + fr2LengthDict[ID] + cdr2LengthDic[ID] + fr3LengthDict[ID]
			longest_tandem = max(tandem_muts, key=lambda x: x[1]) if len(tandem_muts) else (0, 0)
			num_mutations = len(mutations)
			f_num_mutations = float(num_mutations)
			num_tandem_muts = len(tandem_muts)
			expected_tandem_muts = f_num_mutations * (f_num_mutations - 1.0) / float(region_length)
			o.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(ID,
																str(num_mutations),

	with open(tandem_freq_file, 'w') as o:
		for frq in sorted([int(x) for x in tandem_frequency.keys()]):
			o.write("{0}\t{1}\n".format(frq, tandem_frequency[str(frq)]))

	tandem_row = []
	print genes
	print tandem_sum_by_class
	print expected_tandem_sum_by_class
	genes_extra = list(genes)
	genes_extra.append("all")
	for x, y, in zip([tandem_sum_by_class[x] for x in genes_extra], [expected_tandem_sum_by_class[x] for x in genes_extra]):
		if y != 0:
			tandem_row += [x, round(y, 2), round(x / y, 2)]
		else:
			tandem_row += [x, round(y, 2), 0]
	
	"""
	print tandem_row
	tandem_row += tandem_row[-3:]
	print tandem_row
	all_expected_tandem = expected_tandem_sum_by_class["all"]
	all_tandem = tandem_sum_by_class["all"]
	if all_expected_tandem == 0:
		tandem_row[-6:-3] = [all_tandem, round(all_expected_tandem, 2), 0]
	else:
		tandem_row[-6:-3] = [all_tandem, round(all_expected_tandem, 2), round(all_tandem / all_expected_tandem, 2)]
	print tandem_row
	"""
	for i in range(len(genes_extra)):
		gene = genes_extra[i]
		print gene, tandem_row[i*3:i*3+3]

	tandem_freq_file = os.path.join(os.path.dirname(outfile), "shm_overview_tandem_row.txt")
	with open(tandem_freq_file, 'w') as o:
		o.write("Tandems/Expected (ratio),{0}\n".format(",".join([str(x) for x in tandem_row])))

48:c5295dd10dfc

	#tandem mutation stuff
	tandem_frequency = defaultdict(int)
	mutation_frequency = defaultdict(int)
	
	mutations_by_id_dic = {}
	first = True
	mutation_by_id_file = os.path.join(os.path.dirname(outfile), "mutation_by_id.txt")
	with open(mutation_by_id_file, 'r') as mutation_by_id:
		for l in mutation_by_id:
			if first:
				first = False
				continue
			splt = l.split("\t")
			mutations_by_id_dic[splt[0]] = int(splt[1])
    
	tandem_file = os.path.join(os.path.dirname(outfile), "tandems_by_id.txt")
	with open(tandem_file, 'w') as o:
		highest_tandem_length = 0

		o.write("Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n")

				if highest_tandem_length < len(tandem_muts):
					highest_tandem_length = len(tandem_muts)

			region_length = fr1LengthDict[ID] + cdr1LengthDic[ID] + fr2LengthDict[ID] + cdr2LengthDic[ID] + fr3LengthDict[ID]
			longest_tandem = max(tandem_muts, key=lambda x: x[1]) if len(tandem_muts) else (0, 0)
			num_mutations = mutations_by_id_dic[ID] # len(mutations)
			f_num_mutations = float(num_mutations)
			num_tandem_muts = len(tandem_muts)
			expected_tandem_muts = f_num_mutations * (f_num_mutations - 1.0) / float(region_length)
			o.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(ID,
																str(num_mutations),

	with open(tandem_freq_file, 'w') as o:
		for frq in sorted([int(x) for x in tandem_frequency.keys()]):
			o.write("{0}\t{1}\n".format(frq, tandem_frequency[str(frq)]))

	tandem_row = []
	genes_extra = list(genes)
	genes_extra.append("all")
	for x, y, in zip([tandem_sum_by_class[x] for x in genes_extra], [expected_tandem_sum_by_class[x] for x in genes_extra]):
		if y != 0:
			tandem_row += [x, round(y, 2), round(x / y, 2)]
		else:
			tandem_row += [x, round(y, 2), 0]

	tandem_freq_file = os.path.join(os.path.dirname(outfile), "shm_overview_tandem_row.txt")
	with open(tandem_freq_file, 'w') as o:
		o.write("Tandems/Expected (ratio),{0}\n".format(",".join([str(x) for x in tandem_row])))