def test_complex():
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
sos = Agent('SOS1', db_refs={'HGNC': id('SOS1')})
stmt = Complex([egfr, grb2, sos])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
# The graph should contain the node for the complex as well as nodes
# for all of the members
assert len(belgraph) == 4
complex_tuple = [n for n in belgraph.nodes() if n[0] == pc.COMPLEX][0]
# Don't bother to check the tuple, which is now generated by
# PyBEL directly, but check the node data
assert belgraph.node[complex_tuple] == {
pc.FUNCTION: pc.COMPLEX,
pc.MEMBERS: [
{pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'EGFR'},
{pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'GRB2'},
{pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'SOS1'},
]}
def test_rxn_with_controller():
hk1 = Agent('HK1', db_refs={'HGNC': id('HK1')})
glu = Agent('D-GLUCOSE', db_refs={'CHEBI': 'CHEBI:17634'})
g6p = Agent('GLUCOSE-6-PHOSPHATE', db_refs={'CHEBI': 'CHEBI:4170'})
stmt = Conversion(hk1, [glu], [g6p])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
# The graph should contain the node for the reaction as well as nodes
# for all of the members
assert len(belgraph) == 4
rxn_tuple = [n for n in belgraph.nodes() if n[0] == pc.REACTION][0]
# The reaction data should be the same as before
assert belgraph.node[rxn_tuple] == {
pc.FUNCTION: pc.REACTION,
pc.REACTANTS: [
{
pc.FUNCTION: pc.ABUNDANCE,
pc.NAMESPACE: 'CHEBI',
pc.NAME: '17634',
}
],
pc.PRODUCTS: [
{
pc.FUNCTION: pc.ABUNDANCE,
pc.NAMESPACE: 'CHEBI',
pc.NAME: '4170'
}
]
}
def test_inhibition():
braf_kin = Agent('BRAF', activity=ActivityCondition('kinase', True),
db_refs={'HGNC': '1097', 'UP': 'P15056'})
mek = Agent('MAP2K1', db_refs={'HGNC': '6840', 'UP': 'Q02750'})
stmt = Inhibition(braf_kin, mek, 'kinase')
edge = {pc.RELATION: pc.DIRECTLY_DECREASES,
pc.SUBJECT: {
pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'kin',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE}},
pc.OBJECT: {
pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'kin',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE}}}
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph.nodes()) == 2
assert braf_node in belgraph
assert belgraph.node[braf_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'BRAF'}
assert belgraph.node[map2k1_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'MAP2K1'}
assert belgraph.number_of_edges() == 1
_, _, edge_data = list(belgraph.edges(data=True))[0]
assert edge_data == edge
def test_gap():
gap = Agent('RASA1', mods=[ModCondition('phosphorylation')],
db_refs={'HGNC':'9871'})
ras = Agent('KRAS', db_refs={'HGNC':'6407'})
stmt = Gap(gap, ras)
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 3
assert belgraph.number_of_edges() == 2
gap_node = (pc.PROTEIN, 'HGNC', 'RASA1',
(pc.PMOD, (pc.BEL_DEFAULT_NAMESPACE, 'Ph')))
ras_node = (pc.PROTEIN, 'HGNC', 'KRAS')
assert gap_node in belgraph
assert ras_node in belgraph
edge_data = get_edge_data(belgraph, gap_node, ras_node)
edge = {pc.RELATION: pc.DIRECTLY_DECREASES,
pc.SUBJECT: {
pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'gap',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE}},
pc.OBJECT: {
pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'gtp',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE}}}
assert edge_data == edge
def test_increase_amount_tscript():
tp53 = Agent('TP53',
activity=ActivityCondition('transcription', True),
db_refs={'HGNC': '11998'})
mdm2 = Agent('MDM2', db_refs={'HGNC': '6973'})
stmt = IncreaseAmount(tp53, mdm2)
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph.nodes()) == 2
assert mdm2_node in belgraph
assert tp53_node in belgraph
assert belgraph.node[tp53_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'TP53'
}
assert belgraph.node[mdm2_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'MDM2'
}
assert belgraph.number_of_edges() == 1
_, _, edge_data = belgraph.edges(data=True)[0]
assert edge_data[pc.RELATION] == pc.DIRECTLY_INCREASES
assert edge_data[pc.SUBJECT] == {
pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'tscript',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE
}
}
def test_autophosphorylation():
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
stmt = Autophosphorylation(egfr, 'Y', '1173')
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 2
assert egfr_node in belgraph.nodes()
egfr_phos_node = egfr_node + tuple([egfr_phostuple])
assert egfr_phos_node in belgraph.nodes()
assert belgraph.node[egfr_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'EGFR'
}
assert belgraph.node[egfr_phos_node] == {
pc.FUNCTION:
pc.PROTEIN,
pc.NAMESPACE:
'HGNC',
pc.NAME:
'EGFR',
pc.VARIANTS: [{
pc.KIND: pc.PMOD,
pc.IDENTIFIER: {
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE,
pc.NAME: egfr_phostuple[1][1]
},
pc.PMOD_CODE: egfr_phostuple[2],
pc.PMOD_POSITION: egfr_phostuple[3]
}]
}
assert belgraph.number_of_edges() == 2
# There will be two edges between these nodes
edge_dicts = list(
belgraph.get_edge_data(egfr_node, egfr_phos_node).values())
assert {pc.RELATION: pc.DIRECTLY_INCREASES} in edge_dicts
# Test an autophosphorylation with a bound condition
tab1 = Agent('TAB1', db_refs={'HGNC': id('TAB1')})
p38_tab1 = Agent('MAPK14',
bound_conditions=[BoundCondition(tab1)],
db_refs={'HGNC': id('MAPK14')})
stmt = Autophosphorylation(p38_tab1, 'Y', '100')
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 4
assert belgraph.number_of_edges() == 4
def test_bound_condition():
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
ras = Agent('KRAS', db_refs={'HGNC': '6407'})
sos1_bound = Agent(
'SOS1',
mods=[ModCondition('phosphorylation')],
bound_conditions=[BoundCondition(egfr),
BoundCondition(grb2)],
db_refs={'HGNC': id('SOS1')})
stmt = Gef(sos1_bound, ras)
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 6
assert belgraph.number_of_edges() == 5
complex_tuple = [n for n in belgraph.nodes() if n[0] == pc.COMPLEX][0]
# Don't bother to check the tuple, which is now generated by
# PyBEL directly, but check the node data
assert belgraph.node[complex_tuple][pc.FUNCTION] == pc.COMPLEX
complex_members = belgraph.node[complex_tuple][pc.MEMBERS]
members_list = [{
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'EGFR'
}, {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'GRB2'
}, {
pc.FUNCTION:
pc.PROTEIN,
pc.NAMESPACE:
'HGNC',
pc.NAME:
'SOS1',
pc.VARIANTS: [{
pc.KIND: pc.PMOD,
pc.IDENTIFIER: {
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE,
pc.NAME: 'Ph'
}
}]
}]
for member in members_list:
assert member in complex_members
kras_node = (pc.PROTEIN, 'HGNC', 'KRAS')
assert kras_node in belgraph.nodes()
assert (complex_tuple, kras_node) in belgraph.edges()
edge_data = (complex_tuple, kras_node, {
pc.RELATION: pc.DIRECTLY_INCREASES,
pc.OBJECT: {
pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'gtp',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE
}
}
})
assert edge_data in belgraph.edges(data=True)
def test_complex_with_complex():
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
egfr_grb2 = Agent('EGFR', db_refs={'HGNC': id('EGFR')},
bound_conditions=[BoundCondition(grb2)])
sos1_phos = Agent('SOS1',
mods=[ModCondition('phosphorylation', 'Y', '100')],
db_refs={'HGNC': id('SOS1')})
stmt = Complex([sos1_phos, egfr_grb2])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 6
assert belgraph.number_of_edges() == 5
cplx_node_list = [n for n in belgraph.nodes() if n[0] == pc.COMPLEX]
assert len(cplx_node_list) == 2
def test_transphosphorylation():
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
egfr_dimer = Agent('EGFR', bound_conditions=[BoundCondition(egfr)],
db_refs={'HGNC': id('EGFR')})
stmt = Transphosphorylation(egfr_dimer, 'Y', '1173')
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 3
assert belgraph.number_of_edges() == 3
egfr_dimer_node = (pc.COMPLEX, (pc.PROTEIN, 'HGNC', 'EGFR'),
(pc.PROTEIN, 'HGNC', 'EGFR'))
egfr_phos_node = (pc.PROTEIN, 'HGNC', 'EGFR',
(pc.PMOD, (pc.BEL_DEFAULT_NAMESPACE, 'Ph'), 'Tyr', 1173))
edge_data = get_edge_data(belgraph, egfr_dimer_node, egfr_phos_node)
assert edge_data == {pc.RELATION: pc.DIRECTLY_INCREASES}
def test_simple_modification_no_evidence():
braf = Agent('BRAF', db_refs={'HGNC': '1097', 'UP': 'P15056'})
braf_kin = Agent('BRAF', activity=ActivityCondition('kinase', True),
db_refs={'HGNC': '1097', 'UP': 'P15056'})
braf_cat = Agent('BRAF', activity=ActivityCondition('catalytic', True),
db_refs={'HGNC': '1097', 'UP': 'P15056'})
mek = Agent('MAP2K1', db_refs={'HGNC': '6840', 'UP': 'Q02750'})
stmt1 = Phosphorylation(braf, mek, 'S', '218')
stmt2 = Phosphorylation(braf_kin, mek, 'S', '218')
stmt3 = Ubiquitination(braf_cat, mek, 'S', '218')
# Edge info for subject
edge1 = None
edge2 = {pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'kin',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE}}
edge3 = {pc.MODIFIER: pc.ACTIVITY,
pc.EFFECT: {
pc.NAME: 'cat',
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE}}
for stmt, modtuple, subj_edge in ((stmt1, phostuple, edge1),
(stmt2, phostuple, edge2),
(stmt3, ubtuple, edge3)):
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph.nodes()) == 3
assert braf_node in belgraph
map2k1_mod_node = map2k1_node + tuple([modtuple])
assert map2k1_mod_node in belgraph
assert belgraph.node[braf_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'BRAF'}
assert belgraph.node[map2k1_mod_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'MAP2K1',
pc.VARIANTS: [{
pc.KIND: pc.PMOD,
pc.IDENTIFIER: {
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE,
pc.NAME: modtuple[1][1]},
pc.PMOD_CODE: modtuple[2],
pc.PMOD_POSITION: modtuple[3]}]}
assert belgraph.number_of_edges() == 2
edge_data = get_edge_data(belgraph, braf_node, map2k1_mod_node)
assert edge_data.get(pc.SUBJECT) == subj_edge
assert edge_data[pc.RELATION] == pc.DIRECTLY_INCREASES
def test_active_form():
ras = Agent('KRAS', mutations=[MutCondition('12', 'G', 'V')],
db_refs={'HGNC':'6407'})
mapk1_p = Agent('MAP2K1',
mods=[ModCondition('phosphorylation', 'T', '185')],
db_refs={'HGNC': hgnc_client.get_hgnc_id('MAP2K1')})
mapk1_pp = Agent('MAP2K1',
mods=[ModCondition('phosphorylation', 'T', '185'),
ModCondition('phosphorylation', 'Y', '187')],
db_refs={'HGNC': hgnc_client.get_hgnc_id('MAP2K1')})
stmt1 = ActiveForm(ras, 'gtpbound', True)
stmt2 = ActiveForm(mapk1_p, 'kinase', True)
stmt3 = ActiveForm(mapk1_pp, 'kinase', True)
for stmt in (stmt1, stmt2, stmt3):
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 2
def test_complex_with_pmod():
sos1_phos = Agent('SOS1',
mods=[ModCondition('phosphorylation', 'Y', '100')],
db_refs={'HGNC': id('SOS1')})
grb2 = Agent('GRB2', db_refs={'HGNC': id('GRB2')})
egfr = Agent('EGFR', db_refs={'HGNC': id('EGFR')})
stmt = Complex([sos1_phos, grb2, egfr])
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph) == 5
members_list = [{
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'EGFR'
}, {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'GRB2'
}, {
pc.FUNCTION:
pc.PROTEIN,
pc.NAMESPACE:
'HGNC',
pc.NAME:
'SOS1',
pc.VARIANTS: [{
pc.KIND: pc.PMOD,
pc.IDENTIFIER: {
pc.NAMESPACE: pc.BEL_DEFAULT_NAMESPACE,
pc.NAME: 'Ph'
},
pc.PMOD_CODE: 'Tyr',
pc.PMOD_POSITION: 100
}]
}]
# Get the complex node
cplx_node_list = [
n for n in belgraph.nodes(data=True) if n[0][0] == pc.COMPLEX
]
assert len(cplx_node_list) == 1
cplx_node = cplx_node_list[0]
cplx_node_data = cplx_node[1]
# Check the constituents of the complex node
for member in members_list:
assert member in cplx_node_data[pc.MEMBERS]
def test_modification_with_mutation():
braf = Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')],
db_refs={'HGNC': '1097', 'UP': 'P15056'})
mek = Agent('MAP2K1', db_refs={'HGNC': '6840', 'UP': 'Q02750'})
stmt = Phosphorylation(braf, mek, 'S', '218')
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
# Adds in the base protein nodes as well as the variants (so 4 nodes)
assert len(belgraph.nodes()) == 4
braf_mut_node = braf_node + ((pc.HGVS, 'p.Val600Glu'),)
assert braf_mut_node in belgraph
assert belgraph.node[braf_mut_node] == {
pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'BRAF',
pc.VARIANTS: [{
pc.KIND: pc.HGVS,
pc.IDENTIFIER: 'p.Val600Glu'}]}
def test_increase_amount():
tp53 = Agent('TP53', db_refs={'HGNC': '11998'})
mdm2 = Agent('MDM2', db_refs={'HGNC': '6973'})
stmt = IncreaseAmount(tp53, mdm2)
pba = pa.PybelAssembler([stmt])
belgraph = pba.make_model()
assert len(belgraph.nodes()) == 2
assert mdm2_node in belgraph
assert tp53_node in belgraph
assert belgraph.node[tp53_node] == {pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'TP53'}
assert belgraph.node[mdm2_node] == {pc.FUNCTION: pc.PROTEIN,
pc.NAMESPACE: 'HGNC',
pc.NAME: 'MDM2'}
assert belgraph.number_of_edges() == 1
_, _, edge_data = list(belgraph.edges(data=True))[0]
assert edge_data[pc.RELATION] == pc.DIRECTLY_INCREASES
