def test_entry_parsing_only_include_features():
"""genbank entry parsing only include features"""
parsed = parse_genbank(SINGLE_ENTRY, include=["features"])
assert isinstance(parsed, dict)
assert not "locus" in parsed
assert not "division" in parsed
assert not "orientation" in parsed
assert not "strandedness" in parsed
assert not "nucleic_acid" in parsed
assert not "date" in parsed
assert not "definition" in parsed
assert not "accession" in parsed
assert not "version" in parsed
assert not "gi" in parsed
assert not "source" in parsed
assert not "organism" in parsed
assert not "taxonomy" in parsed
assert "features" in parsed
assert 3 == len(parsed["features"])
assert "source" == parsed["features"][0][0]
assert "gene" == parsed["features"][1][0]
assert "CDS" == parsed["features"][2][0]
assert not "sequence" in parsed
def test_entry_parsing_only_include_source():
"""genbank entry parsing only include source"""
parsed = parse_genbank(SINGLE_ENTRY, include=["source"])
assert isinstance(parsed, dict)
assert not "locus" in parsed
assert not "division" in parsed
assert not "orientation" in parsed
assert not "strandedness" in parsed
assert not "nucleic_acid" in parsed
assert not "date" in parsed
assert not "definition" in parsed
assert not "accession" in parsed
assert not "version" in parsed
assert not "gi" in parsed
assert "source" in parsed
assert "Pan troglodytes (chimpanzee)" == parsed["source"]
assert "organism" in parsed
assert "Pan troglodytes" == parsed["organism"]
assert "taxonomy" in parsed
# assert '' == parsed['taxonomy']
assert not "features" in parsed
assert not "sequence" in parsed
def test_entry_parsing_only_include_version():
"""genbank entry parsing only include version"""
parsed = parse_genbank(SINGLE_ENTRY, include=["version"])
assert isinstance(parsed, dict)
assert not "locus" in parsed
assert not "division" in parsed
assert not "orientation" in parsed
assert not "strandedness" in parsed
assert not "nucleic_acid" in parsed
assert not "date" in parsed
assert not "definition" in parsed
assert "accession" in parsed
assert "NM_001071821" == parsed["accession"]
assert "version" in parsed
assert "1" == parsed["version"]
assert "gi" in parsed
assert "115392118" == parsed["gi"]
assert not "source" in parsed
assert not "organism" in parsed
assert not "taxonomy" in parsed
assert not "features" in parsed
assert not "sequence" in parsed
def test_entry_parsing_only_include_locus():
"""genbank entry parsing only include locus"""
parsed = parse_genbank(SINGLE_ENTRY, include=["locus"])
assert isinstance(parsed, dict)
assert "locus" in parsed
assert "NM_001071821" == parsed["locus"]
assert "division" in parsed
assert "PRI" == parsed["division"]
assert "orientation" in parsed
assert "linear" == parsed["orientation"]
assert "strandedness" in parsed
assert "" == parsed["strandedness"]
assert "nucleic_acid" in parsed
assert "mRNA" == parsed["nucleic_acid"]
assert "date" in parsed
assert "09-OCT-2006" == parsed["date"]
assert not "definition" in parsed
assert not "accession" in parsed
assert not "version" in parsed
assert not "gi" in parsed
assert not "source" in parsed
assert not "organism" in parsed
assert not "taxonomy" in parsed
assert not "features" in parsed
assert not "sequence" in parsed
def test_entry_parsing():
"""genbank entry parsing"""
parsed = parse_genbank(SINGLE_ENTRY)
assert isinstance(parsed, dict)
assert "locus" in parsed
assert "NM_001071821" == parsed["locus"]
assert "division" in parsed
assert "PRI" == parsed["division"]
assert "orientation" in parsed
assert "linear" == parsed["orientation"]
assert "strandedness" in parsed
assert "" == parsed["strandedness"]
assert "nucleic_acid" in parsed
assert "mRNA" == parsed["nucleic_acid"]
assert "date" in parsed
assert "09-OCT-2006" == parsed["date"]
assert "definition" in parsed
assert "Pan troglodytes somatic cytochrome c (CYCS), mRNA." == parsed["definition"]
assert "accession" in parsed
assert "NM_001071821" == parsed["accession"]
assert "version" in parsed
assert "1" == parsed["version"]
assert "gi" in parsed
assert "115392118" == parsed["gi"]
assert "source" in parsed
assert "Pan troglodytes (chimpanzee)" == parsed["source"]
assert "organism" in parsed
assert "Pan troglodytes" == parsed["organism"]
assert "taxonomy" in parsed
# assert '' == parsed['taxonomy']
assert "features" in parsed
assert "source" == parsed["features"][0][0]
assert "gene" == parsed["features"][1][0]
assert "CDS" == parsed["features"][2][0]
assert "sequence" in parsed
assert 318 == len(parsed["sequence"])
def test_entry_parsing_only_include_definition():
"""genbank entry parsing only include definition"""
parsed = parse_genbank(SINGLE_ENTRY, include=["definition"])
assert isinstance(parsed, dict)
assert not "locus" in parsed
assert not "division" in parsed
assert not "orientation" in parsed
assert not "strandedness" in parsed
assert not "nucleic_acid" in parsed
assert not "date" in parsed
assert "definition" in parsed
assert "Pan troglodytes somatic cytochrome c (CYCS), mRNA." == parsed["definition"]
assert not "accession" in parsed
assert not "version" in parsed
assert not "gi" in parsed
assert not "source" in parsed
assert not "organism" in parsed
assert not "taxonomy" in parsed
assert not "features" in parsed
assert not "sequence" in parsed
