Default VCF header user Kantale

Documentation

Returns a dictionary and a string representation of a header of Variant Call Format File.

• References
  • Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., Durbin, R., 1000 Genomes Project Analysis Group. Bioinformatics (2011) 27 (15): 2156-2158. The variant call format and VCFtools. http://bioinformatics.oxfordjournals.org/content/27/15/2156.short

Parameters

<inputs>
</inputs>

Return

A tuple that contains the string and the dictionary representation of the default VCF header.

Code

def Default_VCF_header_user_Kantale(header = None, sample_names = None):

	if not header: header = {}

	if not header.has_key("fileformat"): header["fileformat"] = "VCFv4.0"
	if not header.has_key("source"): header["source"] = "PyPedia"
	if not header.has_key("reference"): header["reference"] = "www.pypedia.com"
	if not header.has_key("HEADER"): header["HEADER"] = """CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s""" % (str.join("\t", sample_names))

	header_str = """##fileformat=%s
##source=%s
##reference=%s
#%s
""" % (	header["fileformat"], 
	header["source"], 
	header["reference"], 
	header["HEADER"]) 

	return header, header_str

Unit Tests

def uni1():
	return True

Development Code

def Default_VCF_header_user_Kantale():
	pass

Permissions

Documentation Permissions

Kantale

Code Permissions

Kantale

Unit Tests Permissions

Kantale

Permissions Permissions

Kantale