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 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_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 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_outside_cds_segmented():
p_c = position_convert(
reference_id="NG_012337.1",
from_selector_id=None,
from_coordinate_system=None,
position="27",
to_coordinate_system=None,
to_selector_id="NM_003002.2",
)
assert model_to_string(
p_c["converted_model"]) == "NG_012337.1(NM_003002.2):c.-5035"
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 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_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_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
def test_model_to_string(model, description):
assert model_to_string(model) == description