default_ped_fields = ["family_id", "name", "paternal_id", "maternal_id",

"sex", "phenotype"]

def get_ped_fields(ped_file):

if not ped_file:

return default_ped_fields

with open(ped_file) as in_handle:

possible_header = in_handle.readline()

if possible_header.startswith("#"):

header = possible_header.replace("#", "").split()

# rename the standard fields to a common name

header = default_ped_fields + header[len(default_ped_fields):]

return possible_header.replace("#", "").split()

else:

return default_ped_fields

def load_ped_file(ped_file):

ped_dict = {}

header = get_ped_fields(ped_file)

for line in open(ped_file, 'r'):

if line.startswith("#") or len(line) == 0:

continue

fields = line.split()

ped_dict[fields[1]] = fields

return ped_dict