class TestKamiCorpus(object):
"""Class for testing KAMI model."""
def __init__(self):
"""Initialize test class with a model."""
self.model = KamiCorpus("test")
egfr = Protoform("P00533")
fgfr1 = Protoform("P11362")
fgfr1_pysite = SiteActor(
Protoform("P11362"),
Site("pY",
residues=[Residue("Y", 463, State("phosphorylation", True))]))
abl1_sh2 = RegionActor(Protoform("P00519"), Region("SH2"))
target = Residue("Y", 463, State("phosphorylation", False))
modification = Modification(enzyme=egfr,
substrate=fgfr1,
target=target)
binding = Binding(abl1_sh2, fgfr1_pysite)
self.model.add_interactions([modification, binding])
def test_empty_hierarchy(self):
"""Test getters for various model components."""
model = KamiCorpus("test")
assert (model.action_graph is not None)
assert (len(model.nuggets()) == 0)
assert (model.empty())
model.export_json("test_empty_hierarchy.json")
new_model = KamiCorpus.load_json("test", "test_empty_hierarchy.json")
assert (isinstance(new_model, KamiCorpus))
# assert(new_model._hierarchy == model._hierarchy)
assert (model.mod_template is
model._hierarchy.get_graph("mod_template"))
assert (model.bnd_template is
model._hierarchy.get_graph("bnd_template"))
assert (model.semantic_action_graph is
model._hierarchy.get_graph("semantic_action_graph"))
def test_non_empty_hierarchy(self):
"""."""
model = KamiCorpus("test")
plcg1_pY1253 = Protoform("P19174",
synonyms=["PLCG1"],
residues=[
Residue("Y",
1253,
state=State(
"phosphorylation", True))
])
sh2 = Region(name="SH2")
abl1 = Protoform("P00519", synonyms=["ABL1"])
abl1_sh2 = RegionActor(abl1, sh2)
bnd = Binding(plcg1_pY1253, abl1_sh2)
model.add_interactions([bnd], model)
assert (model.empty() is False)
model.export_json("test_non_empty_hierarchy.json")
new_model = KamiCorpus.load_json("test",
"test_non_empty_hierarchy.json")
assert (isinstance(new_model, KamiCorpus))
assert (("test_action_graph", "meta_model")
in new_model._hierarchy.edges())
# print(model._hierarchy.graphs())
# print(new_model._hierarchy.graphs())
# assert(model._hierarchy == new_model._hierarchy)
def test_add_gene_component(self):
identifier = EntityIdentifier(self.model.action_graph,
self.model.get_action_graph_typing())
protoform = identifier.identify_protoform(Protoform("P00533"))
residue = Residue("Y", 200)
residue_id = self.model.add_residue(residue, protoform)
assert ((residue_id, protoform) in self.model.action_graph.edges())
for region in self.model.get_attached_regions(protoform):
edge = get_edge(self.model.action_graph, region, protoform)
if "start" in edge.keys() and\
"end" in edge.keys() and\
min(edge["start"]) < 200 and\
max(edge["end"]) > 200:
assert ((residue_id, region)
in self.model.action_graph.edges())
for site in self.model.get_attached_sites(protoform):
edge = get_edge(self.model.action_graph, site, protoform)
if "start" in edge.keys() and\
"end" in edge.keys() and\
min(edge["start"]) < 200 and\
max(edge["end"]) > 200:
assert ((residue_id, site) in self.model.action_graph.edges())
site = Site("TestSite", start=200, end=250)
site_id = self.model.add_site(site, protoform, semantics="pY_site")
assert ((site_id, protoform) in self.model.action_graph.edges())
for region in self.model.get_attached_regions(protoform):
edge = get_edge(self.model.action_graph, region, protoform)
if "start" in edge.keys() and\
"end" in edge.keys() and\
min(edge["start"]) < 200 and\
max(edge["end"]) > 250:
assert ((site_id, region) in self.model.action_graph.edges())
for residue in self.model.get_attached_residues(protoform):
edge = get_edge(self.model.action_graph, residue, protoform)
if "loc" in edge.keys() and\
list(edge["loc"])[0] > 200 and\
list(edge["loc"])[0] < 250:
assert ((residue, site_id) in self.model.action_graph.edges())
region = Region("TestRegion", start=100, end=500)
region_id = self.model.add_region(region,
protoform,
semantics="protein_kinase")
for residue in self.model.get_attached_residues(protoform):
edge = get_edge(self.model.action_graph, residue, protoform)
if "loc" in edge.keys() and\
list(edge["loc"])[0] > 100 and\
list(edge["loc"])[0] < 500:
assert ((residue, region_id)
in self.model.action_graph.edges())
for site in self.model.get_attached_sites(protoform):
edge = get_edge(self.model.action_graph, site, protoform)
if "start" in edge.keys() and\
"end" in edge.keys() and\
min(edge["start"]) > 100 and\
max(edge["end"]) < 500:
assert ((site, region_id) in self.model.action_graph.edges())
1092,
state=State(
"phosphorylation",
False)),
value=True,
rate=1,
desc="Phosphorylation of EGFR homodimer")
# Aggregate the interaction object to the corpus
nugget1_id = TEST_CORPUS.add_interaction(interaction1)
# Manually add a new protoform
new_protoform_node = TEST_CORPUS.add_protoform(Protoform("P62993"))
# Manually add a new components to an arbitrary protoform
TEST_CORPUS.add_site(Site("New site"), new_protoform_node)
grb2 = Protoform("P62993",
hgnc_symbol="GRB2",
states=[State("activity", True)])
grb2_sh2 = RegionActor(protoform=grb2, region=Region(name="SH2"))
shc1 = Protoform("P29353", hgnc_symbol="SHC1")
shc1_pY = SiteActor(
protoform=shc1,
site=Site(name="pY",
residues=[Residue("Y", 317, State("phosphorylation", True))]))
interaction1 = Binding(grb2_sh2, shc1)
grb2_sh2_with_residues = RegionActor(protoform=grb2,
region=Region(name="SH2",
class TestIdentifiers(object):
"""Test identifiers of entities in the action graph."""
def __init__(self):
"""Initialize with common hierarchy."""
self.hierarchy = KamiCorpus("test")
protoform = Protoform("A")
self.gene_id = self.hierarchy.add_protoform(protoform)
named_region = Region("Kinase")
interval_region = Region(start=100, end=200)
named_ordered_region1 = Region("SH2", order=1)
named_ordered_region2 = Region("SH2", order=2)
self.named_region = self.hierarchy.add_region(named_region,
self.gene_id)
self.interval_region = self.hierarchy.add_region(
interval_region, self.gene_id)
self.named_ordered_region1 = self.hierarchy.add_region(
named_ordered_region1, self.gene_id)
self.named_ordered_region2 = self.hierarchy.add_region(
named_ordered_region2, self.gene_id)
named_site = Site("ATP binding")
interval_site = Site(start=100, end=200)
named_ordered_site1 = Site("pY", order=1)
named_ordered_site2 = Site("pY", order=2)
self.named_site = self.hierarchy.add_site(named_site, self.gene_id)
self.interval_site = self.hierarchy.add_site(interval_site,
self.gene_id)
self.named_ordered_site1 = self.hierarchy.add_site(
named_ordered_site1, self.gene_id)
self.named_ordered_site2 = self.hierarchy.add_site(
named_ordered_site2, self.gene_id)
residue = Residue("Y", 150)
residue_no_loc = Residue("T")
self.residue = self.hierarchy.add_residue(residue, self.gene_id)
self.residue_no_loc = self.hierarchy.add_residue(
residue_no_loc, self.gene_id)
residue_state = State("activity", True)
site_state = State("activity", True)
region_state = State("activity", True)
gene_state = State("activity", True)
self.residue_state = self.hierarchy.add_state(residue_state,
self.residue)
self.site_state = self.hierarchy.add_state(site_state, self.named_site)
self.region_state = self.hierarchy.add_state(region_state,
self.named_region)
self.gene_state = self.hierarchy.add_state(gene_state, self.gene_id)
def test_identify_protoform(self):
"""Test protoform identification."""
gene1 = Protoform("A")
gene2 = Protoform("B")
identifier = EntityIdentifier(self.hierarchy.action_graph,
self.hierarchy.get_action_graph_typing())
result1 = identifier.identify_protoform(gene1)
result2 = identifier.identify_protoform(gene2)
assert (result1 == self.gene_id)
assert (result2 is None)
def test_identify_region(self):
"""Test region identification."""
identifier = EntityIdentifier(self.hierarchy.action_graph,
self.hierarchy.get_action_graph_typing())
res = identifier.identify_region(Region("Protein kinase"),
self.gene_id)
assert (res == self.named_region)
res = identifier.identify_region(Region(start=101, end=199),
self.gene_id)
assert (res == self.interval_region)
res = identifier.identify_region(Region("SH2"), self.gene_id)
assert (res is None)
res = identifier.identify_region(Region("SH2", order=1), self.gene_id)
assert (res == self.named_ordered_region1)
res = identifier.identify_region(Region("SH2", order=5), self.gene_id)
assert (res is None)
res = identifier.identify_region(
Region("SH2", start=101, end=185, order=2), self.gene_id)
assert (res == self.interval_region)
def test_identify_site(self):
"""Test site identification."""
identifier = EntityIdentifier(self.hierarchy.action_graph,
self.hierarchy.get_action_graph_typing())
res = identifier.identify_site(Site("ATP bind"), self.gene_id)
assert (res == self.named_site)
res = identifier.identify_site(Site("ATP binding site"), self.gene_id)
assert (res == self.named_site)
res = identifier.identify_site(Site(start=101, end=199), self.gene_id)
assert (res == self.interval_site)
res = identifier.identify_site(Site("pY"), self.gene_id)
assert (res is None)
res = identifier.identify_site(Site("pY", order=1), self.gene_id)
assert (res == self.named_ordered_site1)
res = identifier.identify_site(Site("pY", order=5), self.gene_id)
assert (res is None)
res = identifier.identify_site(Site("pY", start=101, end=185, order=2),
self.gene_id)
assert (res == self.interval_site)
def test_identify_residue(self):
"""Test residue identification."""
identifier = EntityIdentifier(self.hierarchy.action_graph,
self.hierarchy.get_action_graph_typing())
res = identifier.identify_residue(Residue("S", 150), self.gene_id)
assert (res == self.residue)
res = identifier.identify_residue(Residue("T"), self.gene_id)
assert (res == self.residue_no_loc)
res = identifier.identify_residue(Residue("S"), self.gene_id)
assert (res is None)
def test_identify_state(self):
"""Test state identification."""
identifier = EntityIdentifier(self.hierarchy.action_graph,
self.hierarchy.get_action_graph_typing())
res = identifier.identify_state(State("activity", False), self.residue)
assert (res == self.residue_state)
res = identifier.identify_state(State("activity", False),
self.named_site)
assert (res == self.site_state)
res = identifier.identify_state(State("activity", False),
self.named_region)
assert (res == self.region_state)
res = identifier.identify_state(State("activity", False), self.gene_id)
assert (res == self.gene_state)