def test_error_position_invalid():
p_c = position_convert(
reference_id="NM_003002.4",
from_selector_id="NM_",
position=100,
)
assert p_c["errors"][0]["code"] == "EPOSITIONINVALID"
def test_info_from_selector_model_identifed_from_reference():
p_c = position_convert(
reference_id="NG_012337.1",
position="100",
to_selector_id="NM_003002.2",
)
assert p_c["infos"][0]["code"] == "ICORRECTEDCOORDINATESYSTEM"
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_error_no_from_selector():
p_c = position_convert(
reference_id="NM_003002.4",
from_selector_id="NM_",
position="100",
)
assert p_c["errors"][0]["code"] == "ENOSELECTORFOUND"
def test_error_invalid_to_selector():
p_c = position_convert(
reference_id="NG_012337.1",
position="100",
to_selector_id="NM_",
)
assert p_c["errors"][0]["code"] == "ENOTOSELECTOR"
def test_info_to_selector_model_identified_from_reference():
p_c = position_convert(
reference_id="NG_012337.1",
from_selector_id="NM_003002.2",
from_coordinate_system="c",
position="100",
)
assert p_c["infos"][0]["code"] == "ITOSELECTORFROMREFERENCE"
def test_error_from_to_selectors_equal_g():
p_c = position_convert(
reference_id="NG_012337.1",
from_coordinate_system="g",
position="100",
to_coordinate_system="g",
)
assert p_c["infos"][0]["code"] == "IFROMTOSELECTORSEQUAL"
def test_error_position_syntax():
p_c = position_convert(
reference_id="NG_012337.1",
from_selector_id="NM_003002.2",
from_coordinate_system="c",
to_coordinate_system="g",
position="100_",
)
assert p_c["errors"][0]["code"] == "EPOSITIONSYNTAX"
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_error_no_required_inputs_reference_id():
p_c = position_convert(
reference_id=None,
position="100",
from_selector_id=None,
from_coordinate_system=None,
to_coordinate_system=None,
to_selector_id=None,
include_overlapping=False,
)
assert get_codes(p_c["errors"]) == {"ENOINPUTS", "ENOINPUTSOTHER"}
def test_error_no_required_inputs_other():
p_c = position_convert(
reference_id="NG_012337.1",
position="100",
from_selector_id=None,
from_coordinate_system=None,
to_coordinate_system=None,
to_selector_id=None,
include_overlapping=False,
)
assert p_c["errors"][0]["code"] == "ENOINPUTSOTHER"
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 get(self):
"""Converts reference positions to selector orientated
positions and vice versa."""
return position_convert(**_args.parse_args())