def test_is_valid_for_vcf_warnings(caplog):
fusion_variant = civic.get_variant_by_id(287)
fusion_variant.is_valid_for_vcf(emit_warnings=True)
assert "Variant 287 has a second set of coordinates. Skipping" in caplog.text
incomplete_coordinates_variant = civic.get_variant_by_id(27)
incomplete_coordinates_variant.is_valid_for_vcf(emit_warnings=True)
assert "Incomplete coordinates for variant 27. Skipping." in caplog.text
unsupported_var_bases_variant = civic.get_variant_by_id(613)
unsupported_var_bases_variant.is_valid_for_vcf(emit_warnings=True)
assert "Unsupported variant base(s) for variant 613. Skipping." in caplog.text
def l158fs():
return civic.get_variant_by_id(2137)
def v2444fs():
return civic.get_variant_by_id(137)
def v273fs():
return civic.get_variant_by_id(762)
def a56fs():
return civic.get_variant_by_id(1785)
def v600e():
return civic.get_variant_by_id(12)
def test_properties(self):
variant = civic.get_variant_by_id(11)
assert sorted(variant.aliases) == sorted(variant.variant_aliases)
assert sorted(variant.groups) == sorted(variant.variant_groups)
assert sorted(variant.types) == sorted(variant.variant_types)
assert variant.summary == variant.description
def test_sanitize_coordinate_bases(self):
variant1 = civic.get_variant_by_id(2696)
variant2 = civic.get_variant_by_id(558)
for v in variant1, variant2:
assert v.coordinates.reference_bases not in ['', '-']
assert v.coordinates.variant_bases not in ['', '-']