def test_format_indel(del_variant, case_obj):
## GIVEN a SV deletion
variant = del_variant
case_id = case_obj['case_id']
## WHEN parsing the variant
formated_variant = build_variant(variant=variant,
case_obj=case_obj,
case_id=case_id)
expected_id = '_'.join(
[variant.CHROM,
str(variant.POS), variant.REF, variant.ALT[0]])
## THEN assert the sv is parsed correct
assert formated_variant
assert formated_variant['variant_id'] == expected_id
assert formated_variant['chrom'] == variant.CHROM
assert formated_variant['end_chrom'] == variant.CHROM
assert formated_variant['pos'] == variant.POS
assert formated_variant['end'] == variant.INFO['END']
assert formated_variant['sv_len'] == abs(variant.INFO['SVLEN'])
assert formated_variant['ref'] == variant.REF
assert formated_variant['alt'] == variant.ALT[0]
assert formated_variant['sv_type'] == 'DEL'
assert formated_variant['case_id'] == case_id
assert formated_variant['homozygote'] == 0
assert formated_variant['hemizygote'] == 0
def variant_obj(request, het_variant, ind_positions, individuals):
_variant_obj = build_variant(variant=het_variant,
individuals=individuals,
ind_positions=ind_positions,
case_id='test',
gq_treshold=None)
return _variant_obj
def load_variants(adapter,
vcf_obj,
case_obj,
skip_case_id=False,
gq_treshold=None,
max_window=3000,
variant_type='snv',
genome_build=None):
"""Load variants for a family into the database.
Args:
adapter (loqusdb.plugins.Adapter): initialized plugin
case_obj(Case): dict with case information
nr_variants(int)
skip_case_id (bool): whether to include the case id on variant level
or not
gq_treshold(int)
max_window(int): Specify the max size for sv windows
variant_type(str): 'sv' or 'snv'
Returns:
nr_inserted(int)
"""
if variant_type == 'snv':
nr_variants = case_obj['nr_variants']
else:
nr_variants = case_obj['nr_sv_variants']
nr_inserted = 0
case_id = case_obj['case_id']
if skip_case_id:
case_id = None
# Loop over the variants in the vcf
with click.progressbar(vcf_obj,
label="Inserting variants",
length=nr_variants) as bar:
variants = (build_variant(variant,
case_obj,
case_id,
gq_treshold,
genome_build=genome_build)
for variant in bar)
if variant_type == 'sv':
for sv_variant in variants:
if not sv_variant:
continue
adapter.add_structural_variant(variant=sv_variant,
max_window=max_window)
nr_inserted += 1
if variant_type == 'snv':
nr_inserted = adapter.add_variants(variants)
LOG.info("Inserted %s variants of type %s", nr_inserted, variant_type)
return nr_inserted
def delete_structural_variants(adapter, vcf_obj, case_obj, case_id=None):
"""Delete structural variants for a case in the database
Args:
adapter(loqusdb.plugins.Adapter)
vcf_obj(iterable(dict))
ind_positions(dict)
case_id(str)
Returns:
nr_deleted (int): Number of deleted variants"""
case_id = case_id or case_obj['case_id']
nr_deleted = 0
start_deleting = datetime.now()
chrom_time = datetime.now()
current_chrom = None
new_chrom = None
for variant in vcf_obj:
formated_variant = build_variant(
variant=variant,
case_obj=case_obj,
case_id=case_id,
)
if not formated_variant:
continue
new_chrom = formated_variant.get('chrom')
adapter.delete_structural_variant(formated_variant)
nr_deleted += 1
if not current_chrom:
LOG.info("Start deleting chromosome {}".format(new_chrom))
current_chrom = new_chrom
chrom_time = datetime.now()
continue
if new_chrom != current_chrom:
LOG.info("Chromosome {0} done".format(current_chrom))
LOG.info("Time to delete chromosome {0}: {1}".format(
current_chrom,
datetime.now() - chrom_time))
LOG.info("Start deleting chromosome {0}".format(new_chrom))
current_chrom = new_chrom
return nr_deleted
def test_format_translocation(translocation_variant, case_obj):
## GIVEN a small insertion (This means that the insertion is included in ALT field)
variant = translocation_variant
case_id = case_obj['case_id']
## WHEN parsing the variant
formated_variant = build_variant(variant=variant,
case_obj=case_obj,
case_id=case_id)
## THEN assert the sv is parsed correct
assert formated_variant['chrom'] == variant.CHROM
assert formated_variant['end_chrom'] == '11'
assert formated_variant['pos'] == variant.POS
assert formated_variant['end'] == 119123896
assert formated_variant['sv_len'] == float('inf')
assert formated_variant['ref'] == variant.REF
assert formated_variant['alt'] == variant.ALT[0]
assert formated_variant['sv_type'] == 'BND'
def test_format_dup_tandem(duptandem_variant, case_obj):
## GIVEN a small insertion (This means that the insertion is included in ALT field)
variant = duptandem_variant
case_id = case_obj['case_id']
## WHEN parsing the variant
formated_variant = build_variant(variant=variant,
case_obj=case_obj,
case_id=case_id)
## THEN assert the sv is parsed correct
assert formated_variant['chrom'] == variant.CHROM
assert formated_variant['end_chrom'] == variant.CHROM
assert formated_variant['pos'] == variant.POS
assert formated_variant['end'] == variant.INFO['END']
assert formated_variant['sv_len'] == abs(variant.INFO['SVLEN'])
assert formated_variant['ref'] == variant.REF
assert formated_variant['alt'] == variant.ALT[0]
assert formated_variant['sv_type'] == 'DUP'
def test_remove_one_SV(self, mongo_adapter, del_variant, case_obj):
# GIVEN a database poulated with one SV
db = mongo_adapter.db
formated_variant = build_variant(del_variant,
case_obj=case_obj,
case_id=case_obj['case_id'])
mongo_adapter.add_structural_variant(formated_variant)
mongo_SV = db.structural_variant.find_one()
mongo_identity = db.identity.find_one()
assert mongo_SV is not None
assert mongo_identity is not None
# WHEN deleting SV
mongo_adapter.delete_structural_variant(formated_variant)
# THEN there should be no remaining SVs in the database
mongo_SV = db.structural_variant.find_one()
mongo_identity = db.indentity.find_one()
assert mongo_SV is None
assert mongo_identity is None
def test_remove_one_of_two_SV(self, mongo_adapter, duptandem_variant,
case_obj):
# GIVEN a database poulated with one SV
db = mongo_adapter.db
formated_variant = build_variant(duptandem_variant,
case_obj=case_obj,
case_id=case_obj['case_id'])
mongo_adapter.add_structural_variant(formated_variant)
# Add second of same variant, changing the start and end position slightly
formated_variant_ = copy.deepcopy(formated_variant)
formated_variant_['pos'] = formated_variant_['pos'] + 2
formated_variant_['end'] = formated_variant_['end'] - 1
formated_variant_['case_id'] = 'case_2'
mongo_adapter.add_structural_variant(formated_variant_)
# This should correspond to one structural variant document
mongo_svs = list(db.structural_variant.find())
assert len(mongo_svs) == 1
mongo_sv = mongo_svs[0]
assert mongo_sv[
'pos_sum'] == formated_variant['pos'] + formated_variant_['pos']
# And two identity documents
mongo_identities = list(db.identity.find())
assert len(mongo_identities) == 2
# WHEN deleting the variant from the first case
mongo_adapter.delete_structural_variant(formated_variant)
# THEN the SV document should have the pos_sum equal to the pos of the
# SV from the second case
mongo_svs = list(db.structural_variant.find())
assert len(mongo_svs) == 1
mongo_sv = mongo_svs[0]
assert mongo_sv['pos_sum'] == formated_variant_['pos']
# And one identity documents
mongo_identities = list(db.identity.find())
assert len(mongo_identities) == 1
def delete_variants(adapter,
vcf_obj,
case_obj,
case_id=None,
genome_build=None):
"""Delete variants for a case in the database
Args:
adapter(loqusdb.plugins.Adapter)
vcf_obj(iterable(dict))
ind_positions(dict)
case_id(str)
Returns:
nr_deleted (int): Number of deleted variants
"""
case_id = case_id or case_obj['case_id']
nr_deleted = 0
start_deleting = datetime.now()
chrom_time = datetime.now()
current_chrom = None
new_chrom = None
variant_list = []
for variant in vcf_obj:
formated_variant = build_variant(variant=variant,
case_obj=case_obj,
case_id=case_id,
genome_build=genome_build)
if not formated_variant:
continue
variant_list.append(formated_variant)
new_chrom = formated_variant.get('chrom')
# When there are enough variants in the variant list
# They are passed to delete_variants
if len(variant_list) == 10000:
adapter.delete_variants(variant_list)
variant_list.clear()
nr_deleted += 1
if not current_chrom:
LOG.info("Start deleting chromosome {}".format(new_chrom))
current_chrom = new_chrom
chrom_time = datetime.now()
continue
if new_chrom != current_chrom:
LOG.info("Chromosome {0} done".format(current_chrom))
LOG.info("Time to delete chromosome {0}: {1}".format(
current_chrom,
datetime.now() - chrom_time))
LOG.info("Start deleting chromosome {0}".format(new_chrom))
current_chrom = new_chrom
if len(variant_list) > 0:
adapter.delete_variants(variant_list)
variant_list.clear()
return nr_deleted
def test_build_het_variant(het_variant, case_obj):
variant_obj = build_variant(variant=het_variant, case_obj=case_obj)
assert variant_obj['chrom'] == het_variant.CHROM
assert variant_obj['homozygote'] == 0
assert variant_obj['hemizygote'] == 0