def test_to_hgvs_locations_simple(hgvs, hgvs_internal_indexing):
r_model = generate_references({
"id": "t1",
"type": "mRNA",
"inverted": False,
"exon": [(3, 6), (8, 13), (16, 21), (24, 26)],
"cds": (10, 19),
})
append_transcript(
r_model,
{
"id": "t2",
"type": "ncRNA",
"inverted": False,
"exon": [(3, 6), (8, 13), (16, 21), (24, 26)],
},
)
model_internal_indexing = to_model(hgvs_internal_indexing)
model_hgvs = to_model(hgvs)
if model_hgvs["coordinate_system"] in ["c", "n"]:
to_selector_id = model_hgvs["reference"]["selector"]["id"]
else:
to_selector_id = None
hgvs_conversion = model_to_string(
to_hgvs_locations(
model=model_internal_indexing,
references=r_model,
to_coordinate_system=model_hgvs["coordinate_system"],
to_selector_id=to_selector_id,
degenerate=True,
))
assert hgvs_conversion == hgvs
def test_outside_cds_description_model():
p_c = position_convert(
description_model=to_model("NG_012337.1:27"),
to_selector_id="NM_003002.2",
)
assert model_to_string(
p_c["converted_model"]) == "NG_012337.1(NM_003002.2):c.-5035"
def _convert_description_to_model(self):
try:
self.input_model = to_model(self.input_description)
except UnexpectedCharacter as e:
self._add_error(errors.syntax_uc(e))
except UnexpectedEnd as e:
self._add_error(errors.syntax_ueof(e))
def test_to_internal_locations(description_in, description_expected,
references):
description_model = to_model(description_in)
description_out = model_to_string(
to_internal_indexing(
to_internal_coordinates(description_model, references)))
assert description_out == description_expected
def get(self, description):
"""Convert a variant description to its dictionary model."""
try:
model = to_model(description)
except Exception:
model = {"errors": "Some unexpected parsing error occured."}
return model
def _get_model_from_segmented_input(self):
description_model = {"reference": {"id": self.reference_id}}
if self.from_selector_id:
description_model["reference"]["selector"] = {
"id": self.from_selector_id
}
if (self.from_coordinate_system
and self.from_coordinate_system.strip().lower()
not in ["selector"]):
description_model[
"coordinate_system"] = self.from_coordinate_system
try:
location_model = to_model(self.position, start_rule="location")
description_model["variants"] = [{"location": location_model}]
except UnexpectedCharacter as e:
self.errors.append(
errors.position_syntax("Unexpected character.", e))
except UnexpectedEnd as e:
self.errors.append(
errors.position_syntax("Unexpected end of input.", e))
self.input_model = description_model
def test_point_shift_from_positive_strand_ro_positive_strand():
model = to_model("NG_012337.1:1005")
model["variants"][0]["location"]["shift"] = 4
p_c = position_convert(
description_model=model,
to_selector_id="NM_003002.2",
)
assert model_to_string(
p_c["converted_model"]) == "NG_012337.1(NM_003002.2):c.-4057"
def test_to_hgvs_locations(description_in, description_expected, references):
model_internal_indexing = to_model(description_in)
model_hgvs = to_model(description_expected)
if model_hgvs["coordinate_system"] in ["c", "n"]:
to_selector_id = model_hgvs["reference"]["selector"]["id"]
else:
to_selector_id = None
hgvs_conversion = model_to_string(
to_hgvs_locations(
model=model_internal_indexing,
references=references,
to_coordinate_system=model_hgvs["coordinate_system"],
to_selector_id=to_selector_id,
degenerate=True,
))
assert hgvs_conversion == description_expected
def test_point_shift_from_positive_strand_to_negative_strand():
"""
NM_012459.2 is on the negative strand on NG_012337.1
"""
model = to_model("NG_012337.1:1005")
model["variants"][0]["location"]["shift"] = 4
p_c = position_convert(
description_model=model,
to_selector_id="NM_012459.2",
)
assert model_to_string(
p_c["converted_model"]) == "NG_012337.1(NM_012459.2):c.*2448"
def lovd_to_bed(input_handle, output_handle, ref, alt):
dialect = Sniffer().sniff(input_handle.read(1024))
input_handle.seek(0)
for record in DictReader(filter(lambda x: x[0] != '#', input_handle),
dialect=dialect):
chrom = 'chr{}'.format(record['{{chromosome}}'])
try:
model = to_model('{}:{}'.format(
chrom, record['{{VariantOnGenome/DNA/hg38}}']))
except (UnexpectedCharacter, UnexpectedEnd):
continue
for variant in model['variants']:
if (variant['type'] == 'substitution'
and variant['deleted'][0]['sequence'] == ref
and variant['inserted'][0]['sequence'] == alt):
output_handle.write('{}\t{}\t{}\n'.format(
chrom, variant['location']['position'] - 1,
variant['location']['position']))
def test_to_internal_coordinates_simple(hgvs, hgvs_internal_indexing):
d_m = to_model(hgvs)
r_model = generate_references({
"id": "t1",
"type": "mRNA",
"inverted": False,
"exon": [(3, 6), (8, 13), (16, 21), (24, 26)],
"cds": (10, 19),
})
append_transcript(
r_model,
{
"id": "t2",
"type": "ncRNA",
"inverted": False,
"exon": [(3, 6), (8, 13), (16, 21), (24, 26)],
},
)
hgvs_internal_indexing_conversion = model_to_string(
to_internal_indexing(to_internal_coordinates(d_m, r_model)))
assert hgvs_internal_indexing_conversion == hgvs_internal_indexing
def test_hgvs_protein_convert(description):
if TESTS.get(description):
assert to_model(description) == TESTS[description]
def test_description_to_model_to_description(description):
"""
Check if the parsed model of a description is converted back to
the initial description.
"""
assert model_to_string(to_model(description)) == description