def test_wrong_string():
"""
Test how the build_vep_string behaves
"""
vep_headers = ["Position", "Type", "Alternative", "Region"]
annotation = [
{"Position":"1", "Type":"nonsynonymous", "Alternative":"C"}
]
with pytest.raises(SyntaxError):
build_vep_string(annotation, vep_headers)
def test_wrong_string():
"""
Test how the build_vep_string behaves
"""
vep_headers = ["Position", "Type", "Alternative", "Region"]
annotation = [{
"Position": "1",
"Type": "nonsynonymous",
"Alternative": "C"
}]
with pytest.raises(SyntaxError):
build_vep_string(annotation, vep_headers)
def test_null_string():
"""
Test how the build_vep_string behaves if no annotations
"""
vep_headers = ["Position", "Type", "Alternative"]
annotation = []
assert build_vep_string(annotation, vep_headers) == ""
def test_null_string():
"""
Test how the build_vep_string behaves if no annotations
"""
vep_headers = ["Position", "Type", "Alternative"]
annotation = []
assert build_vep_string(annotation, vep_headers) == ""
def test_build_vep_string():
"""
Test how the build_vep_string behaves
"""
vep_headers = ["Position", "Type", "Alternative"]
annotation = [
{"Position":"1", "Type":"nonsynonymous", "Alternative":"C"}
]
assert build_vep_string(annotation, vep_headers) == "1|nonsynonymous|C"
def test_build_vep_string():
"""
Test how the build_vep_string behaves
"""
vep_headers = ["Position", "Type", "Alternative"]
annotation = [{
"Position": "1",
"Type": "nonsynonymous",
"Alternative": "C"
}]
assert build_vep_string(annotation, vep_headers) == "1|nonsynonymous|C"
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
