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from gtfparse import expand_attribute_strings
def test_attributes_in_quotes():
attributes = [
"gene_id \"ENSG001\"; tag \"bogotron\"; version \"1\";",
"gene_id \"ENSG002\"; tag \"wolfpuppy\"; version \"2\";"
]
parsed_dict = expand_attribute_strings(attributes)
assert list(sorted(parsed_dict.keys())) == ["gene_id", "tag", "version"]
assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002"]
assert parsed_dict["tag"] == ["bogotron", "wolfpuppy"]
assert parsed_dict["version"] == ["1", "2"]
def test_attributes_without_quotes():
attributes = [
"gene_id ENSG001; tag bogotron; version 1;",
"gene_id ENSG002; tag wolfpuppy; version 2"
]
parsed_dict = expand_attribute_strings(attributes)
assert list(sorted(parsed_dict.keys())) == ["gene_id", "tag", "version"]
assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002"]
assert parsed_dict["tag"] == ["bogotron", "wolfpuppy"]
assert parsed_dict["version"] == ["1", "2"]
def test_optional_attributes():
attributes = [
"gene_id ENSG001; sometimes-present bogotron;",
"gene_id ENSG002;",
"gene_id ENSG003; sometimes-present wolfpuppy;",
]
parsed_dict = expand_attribute_strings(attributes)
assert list(sorted(parsed_dict.keys())) == ["gene_id", "sometimes-present"]
assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002", "ENSG003"]
assert parsed_dict["sometimes-present"] == ["bogotron", "", "wolfpuppy"]
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