Convert VCF to TAB user Kantale

Documentation

Documentation for Convert VCF to TAB

Parameters

<inputs>
</inputs>

Code

def Convert_VCF_to_TAB_user_Kantale(
	input_filename = None,
	output_filename = None,
	print_header = True,
):

	input_file = open(input_filename)
	output_file = open(output_filename, "w")

	header = ["CHROM", "POS", "ID", "REF", "ALT"]

	while True:
		line = input_file.readline()
		if not line:
			break

		ls = line.split()
		if ls[0] == "#CHROM":
			samples_n = len(ls) - 9
			header += ls[9:]
			if print_header:
				output_file.write(str.join("\t", header) + "\n")
			continue

		if ls[0][0] == "#":
			continue

		to_print = [ls[0], ls[1], ls[2], ls[3], ls[4]]
		format = ls[8]
		format_s = format.split(":")
		format_index = format_s.index("GT")
		
		for gtf in ls[9:]:
			gt = gtf.split(":")[format_index]
			
			gt1   = gt[0]
			phase = gt[1]
			gt2   = gt[2]

			tab_gt = []
			for gts in [gt1, gt2]:
				if gts == "0":
					tab_gt += [ls[3]]
				else:
					tab_gt += [ls[4][int(gts)-1]]
			to_print += [str.join(phase, tab_gt)]

		output_file.write(str.join("\t", to_print) + "\n")


	output_file.close()
	input_file.close()

Unit Tests

def uni1():
	return True

Development Code

def Convert_VCF_to_TAB_user_Kantale():
	pass

Permissions

Documentation Permissions

Kantale

Code Permissions

Kantale

Unit Tests Permissions

Kantale

Permissions Permissions

Kantale