def test_sm_missing_exp_empty_ok(self) -> None:
genes = check_variant_links(
small_mutations=[IprGeneVariant({'gene': 'KRAS'})],
copy_variants=[IprGeneVariant({
'gene': 'KRAS',
'variant': ''
})],
expression_variants=[],
structural_variants=[],
)
assert genes == {'KRAS'}
def test_sm_missing_copy(self) -> None:
with mock.patch.object(logger, 'verbose') as mock_debug:
check_variant_links(
small_mutations=[IprGeneVariant({'gene': 'KRAS'})],
copy_variants=[IprGeneVariant({
'gene': 'CDK',
'variant': ''
})],
expression_variants=[
IprGeneVariant({
'gene': 'KRAS',
'variant': ''
})
],
structural_variants=[],
)
assert mock_debug.called
def test_with_valid_inputs(self) -> None:
genes = check_variant_links(
small_mutations=[IprGeneVariant({'gene': 'KRAS'})],
copy_variants=[
IprGeneVariant({
'gene': 'KRAS',
'variant': ''
}),
IprGeneVariant({
'gene': 'CDK',
'variant': ''
}),
],
expression_variants=[
IprGeneVariant({
'gene': 'KRAS',
'variant': ''
})
],
structural_variants=[],
)
assert genes == {'KRAS'}