def convert_data_to_Als(fam_dict):
"""
convert, for a family, the alleles_names data format: from a list to an Als
(like list, just adjusted to alleles_names. see 'Als' class documentation)
:param fam_dict: family dict
"""
for fam_member in fam_dict: # F, M, 1 ...
for allele_name in fam_dict[fam_member]: # A, B ...
al1 = fam_dict[fam_member][allele_name][0] # first allele
al2 = fam_dict[fam_member][allele_name][1] # second allele
new_format = Als() # new object of Als
new_format.extend([al1, al2]) # add alleles_names data
fam_dict[fam_member].update({allele_name: new_format}) # update the data in the dict to be in Als format
def validate(hap_1, hap_2, member, is_serology): # todo: check it !!
"""
compare two haplotype to person (2 from one parent if compare to parent, and 1 from each parent if compare to _child_)
:param hap_1: first haplotype
:param hap_2: second haplotype
:param member: family member
:param is_serology: flag, if serology, the validate is checked in another way
:return: True if consistency, False otherwise
"""
hap_1 = gl_string_to_dict(hap_1)
hap_2 = gl_string_to_dict(hap_2)
if not is_serology:
for allele_name, allele_values in member.items():
val_member1, val_member2, val_hap1, val_hap2 = \
allele_values[0], allele_values[1], hap_1[allele_name], hap_2[allele_name]
success_option1 = is_equal(val_member1, val_hap1) and is_equal(
val_member2, val_hap2)
success_option2 = is_equal(val_member1, val_hap2) and is_equal(
val_member2, val_hap1)
if not (success_option1 or success_option2):
return False
return True
else: # serology data. could be more than 2 options in 'member[allele_name]'
pairs_consistent = [False] * len(member.keys())
for idx_allele, (allele_name,
allele_values) in enumerate(member.items()):
val_hap1, val_hap2 = hap_1[allele_name], hap_2[allele_name]
val_member = Als()
val_member.extend(member[allele_name])
# the first two conditions are for [] and ["", ""]
if not val_member or not any(
val_member
) or val_hap1 in val_member and val_hap2 in val_member:
pairs_consistent[idx_allele] = True
continue
if all(pairs_consistent):
return True
return False