def test_reserved_attributes(self, test_data_dir, tmp_path):
gb = test_data_dir / "INSC1020_subset_gff3.gb"
parsed = list(parse_genbank(gb))
a = [x.to_annotation_collection() for x in parsed]
tmp_gff = tmp_path / "tmp.gff"
with pytest.warns(ReservedKeyWarning):
with open(tmp_gff, "w") as fh:
collection_to_gff3(a, fh, raise_on_reserved_attributes=False)
with pytest.raises(GFF3ExportException):
with open(tmp_gff, "w") as fh:
collection_to_gff3(a, fh, raise_on_reserved_attributes=True)
def test_gff3_strand_error(self, tmp_path):
tmp_gff3 = tmp_path / "tmp.gff3"
annot = self.annot.to_annotation_collection().to_dict()
annot["feature_collections"][0]["feature_intervals"][0][
"strand"] = "MINUS"
annot = AnnotationCollectionModel.Schema().load(
annot).to_annotation_collection()
with open(tmp_gff3, "w") as fh:
collection_to_gff3([annot], fh)
with pytest.raises(GFF3ChildParentMismatchError):
_ = list(parse_standard_gff3(tmp_gff3))
def test_to_gff(self, test_data_dir, tmp_path):
"""Parse GFF, write to disk, parse, compare"""
gff = test_data_dir / "INSC1006_chrI.gff3"
parsed = list(parse_standard_gff3(gff))
a = [x.to_annotation_collection() for x in parsed]
tmp_gff = tmp_path / "tmp.gff"
with open(tmp_gff, "w") as fh:
collection_to_gff3(a, fh)
gff2 = list(parse_standard_gff3(tmp_gff))
a2 = [x.to_annotation_collection() for x in gff2]
for c1, c2 in zip(a, a2):
assert c1.to_dict() == c2.to_dict()
def test_genbank_to_gff(self, test_data_dir, tmp_path, gbk, gff3, add_sequences):
"""
INSC1006_chrI.gff3 and INSC1003.gff3 were created from INSC1006_chrI.gbff and INSC1003.gbk
respectively, so we can compare to the source file.
"""
gbk = test_data_dir / gbk
with open(gbk, "r") as fh:
parsed = list(ParsedAnnotationRecord.parsed_annotation_records_to_model(parse_genbank(fh)))
tmp_gff = tmp_path / "tmp.gff"
with open(tmp_gff, "w") as fh:
collection_to_gff3(parsed, fh, add_sequences=add_sequences)
for l1, l2 in zip(open(tmp_gff), open(test_data_dir / gff3)):
assert l1 == l2