def test_parse_broken_qualifier(self):
# test if wrong separator between GO ID and description (semicolon instead of colon) is caught
broken_qualifier = [
"GO:0004871: signal transducer activity",
"GO:0007165; signal transduction"
]
with self.assertRaisesRegex(ValueError, "Cannot parse qualifier"):
GOQualifier.from_biopython(broken_qualifier)
def from_biopython(bio_feature: SeqFeature, feature: "PFAMDomain" = None, # type: ignore
leftovers: Dict[str, List[str]] = None) -> "PFAMDomain":
if leftovers is None:
leftovers = Feature.make_qualifiers_copy(bio_feature)
# grab mandatory qualifiers and create the class
description = leftovers.pop("description")[0]
p_start = int(leftovers.pop("protein_start")[0])
p_end = int(leftovers.pop("protein_end")[0])
xref = leftovers.get("db_xref", []) # only remove the interesting part
name = None
for i, ref in enumerate(xref):
if ref.startswith("PF"):
name = ref
xref.pop(i)
break
if name is None:
raise SecmetInvalidInputError("PFAMDomain missing identifier")
tool = leftovers.pop("aSTool")[0]
feature = PFAMDomain(bio_feature.location, description, p_start, p_end,
identifier=name, tool=tool)
# grab optional qualifiers
feature.gene_ontologies = GOQualifier.from_biopython(leftovers.pop("gene_ontologies", []))
if "probability" in leftovers:
feature.probability = float(leftovers["probability"][0])
# grab parent optional qualifiers
updated = super(PFAMDomain, feature).from_biopython(bio_feature, feature=feature, leftovers=leftovers)
assert isinstance(updated, PFAMDomain)
return updated
def test_biopython_to_and_from(self):
original = GOQualifier({
'GO:0004871': 'signal transducer activity',
'GO:0007165': 'signal transduction',
'GO:0016020': 'membrane'
})
new = GOQualifier.from_biopython(original.to_biopython())
assert original.go_entries == new.go_entries
def from_biopython(cls: Type[T],
bio_feature: SeqFeature,
feature: T = None,
leftovers: Dict[str, List[str]] = None,
record: Any = None) -> T:
if leftovers is None:
leftovers = Feature.make_qualifiers_copy(bio_feature)
# grab mandatory qualifiers and create the class
description = leftovers.pop("description")[0]
p_start = int(leftovers.pop("protein_start")[0])
p_end = int(leftovers.pop("protein_end")[0])
xref = leftovers.get("db_xref", []) # only remove the interesting part
name = None
for i, ref in enumerate(xref):
if ref.startswith("PF"):
name = ref
xref.pop(i)
break
if name is None:
raise SecmetInvalidInputError("PFAMDomain missing identifier")
tool = leftovers.pop("aSTool")[0]
locus_tag = leftovers.pop("locus_tag", ["(unknown)"])[0]
feature = cls(bio_feature.location,
description,
FeatureLocation(p_start, p_end),
identifier=name,
tool=tool,
locus_tag=locus_tag)
# grab optional qualifiers
feature.gene_ontologies = GOQualifier.from_biopython(
leftovers.pop("gene_ontologies", []))
# grab parent optional qualifiers
updated = super().from_biopython(bio_feature,
feature=feature,
leftovers=leftovers,
record=record)
assert isinstance(updated, PFAMDomain)
return updated