"""Parse input PED files for loading into GEMINI sample table.

Tries to parse as tab-delimited if files contain tabs, otherwise splits

on whitespace.

"""

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

"sex", "phenotype"]

missing_member = set(["None", None, "0", "-9"])

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("#"):

if possible_header.count("\t") > 1:

header = possible_header.replace("#", "").rstrip().split("\t")

else:

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

# rename the standard fields to a common name

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

return header

else:

return default_ped_fields

def load_ped_file(ped_file):

ped_dict = {}

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

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

continue

parts = line.rstrip().split("\t") if line.count("\t") > 1 else line.split()

fields = [x.strip() for x in _fix_ped_family_fields(parts)]

fields = _fix_ped_affected(fields)

fields = _fix_ped_sex(fields)

ped_dict[fields[1]] = fields

return ped_dict

def _fix_ped_sex(fields):

l = {'male': '1', 'female': '2'}

fields[4] = l.get(fields[4].lower(), fields[4])

return fields

def _fix_ped_affected(fields):

l = {'affected': '2', 'unaffected': '1'}

fields[5] = l.get(fields[5].lower(), fields[5])

return fields

def _fix_ped_family_fields(fields):

"""

translate commonly used values for missing family members to the canonical

0 == missing style used in the PED spec

"""

family_fields = [0, 2, 3]

for field in family_fields:

if fields[field] in missing_member:

fields[field] = "0"

return fields