def test_split_partial_alternative_gt_call():
"""
Test how split_genotype behaves when only ref allele is called
"""
genotype = "2|.:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == "0|.:30"
assert second_genotype == "1|.:30"
assert third_genotype == "0|.:30"
def test_split_partial_reference_gt_call():
"""
Test how split_genotype behaves when only ref allele is called
"""
genotype = ".|2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == ".|0:30"
assert second_genotype == ".|1:30"
assert third_genotype == ".|0:30"
def test_other_allele_symbol():
"""
Test how split_genotype behaves
"""
genotype = "1/2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == "./1:30"
assert second_genotype == "./1:30"
assert third_genotype == "./.:30"
def test_other_gt_delimiter():
"""
Test how split_genotype behaves with '|' as delimiter
"""
genotype = "1|2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == ".|1:30"
assert second_genotype == ".|1:30"
assert third_genotype == ".|.:30"
def test_simple_split_ad():
"""
Test how split_genotype behaves with allele depth
"""
genotype = "1/2:30:0,10,20"
gt_format = "GT:DP:AD"
first_genotype = split_genotype(genotype, gt_format, 0)
second_genotype = split_genotype(genotype, gt_format, 1)
third_genotype = split_genotype(genotype, gt_format, 2)
assert first_genotype == "0/1:30:0,10"
assert second_genotype == "0/1:30:0,20"
assert third_genotype == "0/0:30:0,0"
def test_simple_split():
"""
Test how split_genotype behaves
"""
genotype = "1/2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0)
second_genotype = split_genotype(genotype, gt_format, 1)
third_genotype = split_genotype(genotype, gt_format, 2)
assert first_genotype == "0/1:30"
assert second_genotype == "0/1:30"
assert third_genotype == "0/0:30"
def test_split_partial_alternative_gt_call():
"""
Test how split_genotype behaves when only ref allele is called
"""
genotype = "2|.:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == "0|.:30"
assert second_genotype == "1|.:30"
assert third_genotype == "0|.:30"
def test_other_gt_delimiter():
"""
Test how split_genotype behaves with '|' as delimiter
"""
genotype = "1|2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == ".|1:30"
assert second_genotype == ".|1:30"
assert third_genotype == ".|.:30"
def test_other_allele_symbol():
"""
Test how split_genotype behaves
"""
genotype = "1/2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == "./1:30"
assert second_genotype == "./1:30"
assert third_genotype == "./.:30"
def test_simple_split():
"""
Test how split_genotype behaves
"""
genotype = "1/2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0)
second_genotype = split_genotype(genotype, gt_format, 1)
third_genotype = split_genotype(genotype, gt_format, 2)
assert first_genotype == "0/1:30"
assert second_genotype == "0/1:30"
assert third_genotype == "0/0:30"
def test_simple_split_ad():
"""
Test how split_genotype behaves with allele depth
"""
genotype = "1/2:30:0,10,20"
gt_format = "GT:DP:AD"
first_genotype = split_genotype(genotype, gt_format, 0)
second_genotype = split_genotype(genotype, gt_format, 1)
third_genotype = split_genotype(genotype, gt_format, 2)
assert first_genotype == "0/1:30:0,10"
assert second_genotype == "0/1:30:0,20"
assert third_genotype == "0/0:30:0,0"
def test_split_partial_reference_gt_call():
"""
Test how split_genotype behaves when only ref allele is called
"""
genotype = ".|2:30"
gt_format = "GT:DP"
first_genotype = split_genotype(genotype, gt_format, 0, '.')
second_genotype = split_genotype(genotype, gt_format, 1, '.')
third_genotype = split_genotype(genotype, gt_format, 2, '.')
assert first_genotype == ".|0:30"
assert second_genotype == ".|1:30"
assert third_genotype == ".|0:30"
def split_variants(variant_dict, header_parser, allele_symbol='0'):
"""
Checks if there are multiple alternative alleles and splitts the
variant.
If there are multiple alternatives the info fields, vep annotations
and genotype calls will be splitted in the correct way
Args:
variant_dict: a dictionary with the variant information
Yields:
variant: A variant dictionary with the splitted information for each
alternative
"""
logger = getLogger(__name__)
logger.info("Allele symbol {0}".format(allele_symbol))
alternatives = variant_dict['ALT'].split(',')
reference = variant_dict['REF']
number_of_values = 1
# Go through each of the alternative alleles:
for alternative_number, alternative in enumerate(alternatives):
variant = {}
info_dict = OrderedDict()
# This is a dict on the form {ALT:[{vep_info_dict}]}
vep_dict = {}
genotype_dict = {}
variant['CHROM'] = variant_dict['CHROM']
variant['POS'] = variant_dict['POS']
try:
# There will not allways be one rsID for each alternative
variant['ID'] = variant_dict['ID'].split(';')[alternative_number]
# If only one id is present for multiple alleles they all get the same ID
except IndexError:
variant['ID'] = variant_dict['ID']
variant['REF'] = variant_dict['REF']
variant['ALT'] = alternative
variant['QUAL'] = variant_dict['QUAL']
variant['FILTER'] = variant_dict['FILTER']
if 'FORMAT' in variant_dict:
gt_format = variant_dict['FORMAT']
variant['FORMAT'] = gt_format
for info in variant_dict['info_dict']:
if info and info != '.':
# Check if the info field have one entry per allele:
number_of_values = header_parser.extra_info[info]['Number']
if info == 'CSQ':
vep_dict[alternative] = variant_dict['vep_info'][alternative]
if vep_dict[alternative]:
info_dict['CSQ'] = [
build_vep_string(
vep_dict[alternative],
header_parser.vep_columns
)
]
# If there is one value per allele we need to split it in
# the proper way
elif number_of_values == 'A':
try:
# When we split the alleles we only want to annotate with the correct number
info_dict[info] = [variant_dict['info_dict'][info][alternative_number]]
except IndexError:
# If there is only one annotation we choose that one
info_dict[info] = [variant_dict['info_dict'][info][0]]
# Choose the right vep info from the old variant
elif number_of_values == 'R':
reference_value = variant_dict['info_dict'][info][0]
new_info = [reference_value]
try:
# When we split the alleles we only want to annotate with the correct number
allele_value = variant_dict['info_dict'][info][alternative_number + 1]
new_info.append(allele_value)
info_dict[info] = new_info
except IndexError:
# If annotation is missing we keep the original annotation
info_dict[info] = variant_dict['info_dict'][info]
else:
info_dict[info] = variant_dict['info_dict'][info]
else:
info_dict[info] = []
variant['INFO'] = build_info_string(info_dict)
for individual in variant_dict['genotypes']:
new_genotype = split_genotype(
variant_dict[individual],
variant['FORMAT'],
alternative_number,
allele_symbol
)
variant[individual] = new_genotype
genotype_dict[individual] = Genotype(**dict(zip(gt_format.split(':'), variant[individual].split(':'))))
variant['info_dict'] = info_dict
variant['vep_info'] = vep_dict
variant['genotypes'] = genotype_dict
variant['variant_id'] = '_'.join([variant['CHROM'],
variant['POS'],
variant['REF'],
alternative])
yield variant
