From impute2 to beagle user Kantale

Documentation

Converts an output from impute2 execution to a single beagle probabilities file

Parameters

<inputs>
</inputs>

Code

def From_impute2_to_beagle_user_Kantale(
	filenames = None,
	dir_name = None,
	pattern_name = None,
	output_filename = None,
	beagle_header_filename = None
	):

	output_file = open(output_filename, "w")

	if beagle_header_filename:
		f = open(beagle_header_filename, "U")
		while True:
			line = f.readline()
			line_splitted = line.split()
			if line_splitted[0] == "marker":
				output_file.write(line)
				break


	list_of_files = []
	if dir_name:
		list_of_files = os.listdir(dir_name)
		if pattern_name:
			list_of_files = [x for x in list_of_files if fnmatch.fnmatch(x, pattern_name)]

	if filenames:
		list_of_files = filenames

	for filename in filenames:
		print "Converting.. ", filename
		input_file = open(filename, "U")
		while True:
			line = input_file.readline()
			if not line: break

			line_splitted = line.replace("\n", "").split()
			to_print = [line_splitted[1]] + line_splitted[3:]
			output_file.write(  str.join(" ", to_print)  +  "\n"   )
				

	output_file.close()

Unit Tests

def uni1():
	return True

Development Code

def From_impute2_to_beagle_user_Kantale():
	pass

Permissions

Documentation Permissions

Kantale

Code Permissions

Kantale

Unit Tests Permissions

Kantale

Permissions Permissions

Kantale