def test_bioentities_get_when_exists():
e = collections.BioEntities({
Curie("FOO", "123"):
Subject(Curie("FOO", "123"), "hello", "world", [], "protien",
Curie("NCBITaxon", "12345"))
})
assert e.get(Curie.from_str("FOO:123")) == Subject(
Curie("FOO", "123"), "hello", "world", [], "protien",
Curie("NCBITaxon", "12345"))
def test_bioentities_load_from_file():
pombase = collections.BioEntities.load_from_file(
"tests/resources/truncated-pombase.gpi")
assert len(pombase.entities.keys()) == 199 # Has 199 gpi lines in the file
assert pombase.get(Curie.from_str("PomBase:SPAC1565.04c")) == Subject(
Curie.from_str("PomBase:SPAC1565.04c"), "ste4", "adaptor protein Ste4",
[], "protein", Curie.from_str("NCBITaxon:4896"))
def test_bioentities_merge_clobber():
e = collections.BioEntities({
Curie("FOO", "123"):
Subject(Curie("FOO", "123"), "hello", "world", [], "protien",
Curie("NCBITaxon", "12345"))
})
o = collections.BioEntities({
Curie("FOO", "123"):
Subject(Curie("FOO", "123"), "different", "world", [], "dog",
Curie("NCBITaxon", "12345"))
})
# Get the clobbered key, the value should be the subject in `o`
assert e.merge(o).get(Curie("FOO",
"123")) == Subject(Curie("FOO",
"123"), "different",
"world", [], "dog",
Curie("NCBITaxon", "12345"))
def test_bioentities_merge():
e = collections.BioEntities({
Curie("FOO", "123"):
Subject(Curie("FOO", "123"), "hello", "world", [], "protien",
Curie("NCBITaxon", "12345"))
})
o = collections.BioEntities({
Curie("BAR", "987"):
Subject(Curie("BAR", "987"), "goodbye", "world", [], "protien",
Curie("NCBITaxon", "999"))
})
assert e.merge(o) == collections.BioEntities({
Curie("FOO", "123"):
Subject(Curie("FOO", "123"), "hello", "world", [], "protien",
Curie("NCBITaxon", "12345")),
Curie("BAR", "987"):
Subject(Curie("BAR", "987"), "goodbye", "world", [], "protien",
Curie("NCBITaxon", "999"))
})
def test_bioentities_from_gpi_2_0():
entities = collections.BioEntities.load_from_file(
"tests/resources/mgi.truncated.gpi2")
assert entities.get(Curie(
namespace="MGI", identity="MGI:1918925")) == Subject(
id=Curie.from_str("MGI:MGI:1918925"),
label="0610010F05Rik",
fullname=["RIKEN cDNA 0610010F05 gene"],
synonyms=[],
type=[Curie.from_str("SO:0001217")],
taxon=Curie(namespace="NCBITaxon", identity="10090"),
db_xrefs=[Curie.from_str("UniProtKB:Q68FF0")])
def test_gaf_writer():
association = GoAssociation(
source_line="",
subject=Subject(
id=Curie("PomBase", "SPAC25B8.17"),
label="ypf1",
type=["protein"],
fullname=[
"intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)"
],
synonyms=["ppp81"],
taxon=Curie("NCBITaxon", "4896")),
object=Term(id=Curie("GO", "0000006"),
taxon=Curie("NCBITaxon", "4896")),
negated=False,
qualifiers=[],
aspect=Aspect("C"),
relation=Curie("BFO", "0000050"),
interacting_taxon=Curie("NCBITaxon", "555"),
evidence=Evidence(
type=Curie("ECO", "0000266"),
has_supporting_reference=[Curie("GO_REF", "0000024")],
with_support_from=[
ConjunctiveSet(elements=[Curie("SGD", "S000001583")])
]),
provided_by=Provider("PomBase"),
date=Date(year="2015", month="03", day="05", time=""),
subject_extensions=[
ExtensionUnit(relation=Curie("rdfs", "subClassOf"),
term=Curie("UniProtKB", "P12345"))
],
object_extensions=[
ConjunctiveSet(elements=[
ExtensionUnit(relation=Curie("BFO", "0000050"),
term=Curie("X", "1"))
])
],
properties=dict())
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
# `out` will get written with gaf lines from the above assocation object
expected = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896|taxon:555\t20150305\tPomBase\tpart_of(X:1)\tUniProtKB:P12345"
writer.write_assoc(association)
print(out.getvalue())
gaf = [
line.strip("\n") for line in out.getvalue().split("\n")
if not line.startswith("!")
][0]
assert expected == gaf
def load_from_file(BioEntities, path: str):
entities = dict() # type: Dict[Curie, Subject]
try:
gpi_parser = entityparser.GpiParser()
with open(path) as gpi:
for line in gpi:
_, ents = gpi_parser.parse_line(line)
for entity in ents:
# entity will be a well-formed curie
entity_id = Curie.from_str(entity["id"])
entities[entity_id] = Subject(
entity_id, entity["label"], entity["full_name"],
entity["synonyms"], entity["type"],
Curie.from_str(entity["taxon"]["id"]))
except Exception as e:
logger.error("Failed to read GPI file: {}".format(str(e)))
return BioEntities(entities)