def test_distinct(self):
filepath = os.path.join("gffparser", "test", "data", "distinct_cds_same_parent.gff3")
record = parse_gff(filepath)[0]
assert len(record.cds_features) == 2
assert record.cds_features[0].gff_id != record.cds_features[1].gff_id
assert isinstance(record.cds_features[0].location, FeatureLocation)
assert isinstance(record.cds_features[1].location, FeatureLocation)
def test_RNA_gene(self):
filepath = os.path.join("gffparser", "test", "data", "RNA_gene.gff3")
record = parse_gff(filepath)[0]
gene = record.parent_features["A"]
assert len(gene.generics) == 1
assert gene.gff_type == "RNA_gene"
rna = record.parent_features["B"]
assert rna.parent == gene
def test_indistinct(self):
filepath = os.path.join("gffparser", "test", "data", "indistinct_cds_same_parent.gff3")
record = parse_gff(filepath)[0]
assert len(record.cds_features) == 1
assert isinstance(record.cds_features[0].location, CompoundLocation)
def test_wrong_ordering(self):
filepath = os.path.join("gffparser", "test", "data", "out_of_order_parent.gff3")
record = parse_gff(filepath)[0]
gene = record.parent_features["gene"]
cds = record.cds_features[0]
assert cds.parent == gene
def test_simple(self):
filepath = os.path.join("gffparser", "test", "data", "simple_parent.gff3")
record = parse_gff(filepath)[0]
gene = record.parent_features["gene"]
cds = record.cds_features[0]
assert cds.parent == gene