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="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="PomBase",
date="20150305",
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 test_bioentities_get_when_empty():
e = collections.BioEntities(dict())
assert e.get(Curie("FOO", "123")) == None
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_conjunctive_set_str_to_conjunctions():
c = association.ConjunctiveSet.str_to_conjunctions("")
assert c == []
c = association.ConjunctiveSet.str_to_conjunctions("MGI:12345")
assert c == [association.ConjunctiveSet([Curie.from_str("MGI:12345")])]
c = association.ConjunctiveSet.str_to_conjunctions("MGI:12345,MGI:12345")
assert c == [
association.ConjunctiveSet(
[Curie.from_str("MGI:12345"),
Curie.from_str("MGI:12345")])
]
c = association.ConjunctiveSet.str_to_conjunctions("MGI:12345|MGI:12345")
assert c == [
association.ConjunctiveSet([Curie.from_str("MGI:12345")]),
association.ConjunctiveSet([Curie.from_str("MGI:12345")])
]
c = association.ConjunctiveSet.str_to_conjunctions(
"MGI:12345,DOI:333|GO:987")
assert c == [
association.ConjunctiveSet(
[Curie.from_str("MGI:12345"),
Curie.from_str("DOI:333")]),
association.ConjunctiveSet([Curie.from_str("GO:987")])
]
c = association.ConjunctiveSet.str_to_conjunctions(
"part_of(MGI:123),part_of(FOO:456)|has_direct_input(BAR:987)",
conjunct_element_builder=lambda u: association.ExtensionUnit.from_str(
u))
assert c == [
association.ConjunctiveSet([
association.ExtensionUnit(Curie.from_str("BFO:0000050"),
Curie.from_str("MGI:123")),
association.ExtensionUnit(Curie.from_str("BFO:0000050"),
Curie.from_str("FOO:456"))
]),
association.ConjunctiveSet([
association.ExtensionUnit(Curie.from_str("GOREL:0000752"),
Curie.from_str("BAR:987"))
])
]
c = association.ConjunctiveSet.str_to_conjunctions(
"HECK_NO,part_of(FOO:456)|has_direct_input(BAR:987)",
conjunct_element_builder=lambda u: association.ExtensionUnit.from_str(
u))
assert c == association.Error("HECK_NO")
def test_subject_types_label():
s = association.Subject(Curie.from_str("HELLO:12345"), "Hello object",
["fullname"], [], ["mRNA", "tRNA"],
association.Curie.from_str("NCBITaxon:12345"))
assert [Curie.from_str("SO:0000234"),
Curie.from_str("SO:0000253")] == s.type
def test_subject_types_unknown():
s = association.Subject(Curie.from_str("HELLO:12345"), "Hello object",
["fullname"], [], [],
association.Curie.from_str("NCBITaxon:12345"))
assert [Curie(namespace="CHEBI", identity="33695")] == s.type