def test_process_row_dephos_nores_up():
test_row = _SignorRow_(ENTITYA='STK11', TYPEA='protein', IDA='Q15831',
DATABASEA='UNIPROT', ENTITYB='AMPK', TYPEB='complex',
IDB='SIGNOR-C15', DATABASEB='SIGNOR',
EFFECT='up-regulates activity', MECHANISM='dephosphorylation',
RESIDUE='', SEQUENCE='', TAX_ID='-1', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='',
MODASEQ='', MODIFICATIONB='', MODBSEQ='', PMID='14976552',
DIRECT='YES', NOTES='', ANNOTATOR='lperfetto',
SENTENCE='', SIGNOR_ID='SIGNOR-242602')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == False
def test_complexes_with_families():
test_row = _SignorRow_(ENTITYA='MAPK1', TYPEA='protein',
IDA='P27361', DATABASEA='UNIPROT', ENTITYB='CDO/JLP/P38',
TYPEB='complex', IDB='SIGNOR-C22', DATABASEB='SIGNOR',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional regulation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0002314',
TISSUE_DATA='BTO:0000887;BTO:0001103', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='22863532', DIRECT='NO', NOTES='',
ANNOTATOR='miannu', SENTENCE='', SIGNOR_ID='SIGNOR-198641')
complex_map = {'SIGNOR-C22' : ['O60271', 'Q4KMG0', 'SIGNOR-PF14']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 2
assert isinstance(sp.statements[0], IncreaseAmount)
obj = sp.statements[0].obj
assert obj.db_refs['UP'] == 'O60271'
assert len(obj.bound_conditions) == 2
assert obj.bound_conditions[0].agent.db_refs['UP'] == 'Q4KMG0'
assert obj.bound_conditions[1].agent.db_refs['SIGNOR'] == 'SIGNOR-PF14'
assert obj.bound_conditions[1].agent.db_refs['FPLX'] == 'ROBO'
s1 = sp.statements[1]
assert isinstance(s1, Complex)
members = s1.members
assert members[0].db_refs['UP'] == 'O60271'
assert members[1].db_refs['UP'] == 'Q4KMG0'
assert members[2].db_refs['SIGNOR'] == 'SIGNOR-PF14'
assert members[2].db_refs['FPLX'] == 'ROBO'
def test_process_row_chem_inh():
test_row_chem_inh = _SignorRow_(ENTITYA='722544-51-6',
TYPEA='chemical',
IDA='CID:16007391',
DATABASEA='PUBCHEM',
ENTITYB='AURKB',
TYPEB='protein',
IDB='Q96GD4',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='chemical inhibition',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='Other',
DIRECT='YES',
NOTES='Selleck',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-190245')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_inh)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Inhibition)
def test_process_row_stab():
test_row_stab = _SignorRow_(ENTITYA='UCHL5',
TYPEA='protein',
IDA='Q9Y5K5',
DATABASEA='UNIPROT',
ENTITYB='TGFBR1',
TYPEB='protein',
IDB='P36897',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='stabilization',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='17052192',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-150135')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_stab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
def test_process_row_complex_down():
test_row = _SignorRow_(ENTITYA='XIAP', TYPEA='protein', IDA='P98170',
DATABASEA='UNIPROT', ENTITYB='CASP3', TYPEB='protein',
IDB='P42574', DATABASEB='UNIPROT', EFFECT='down-regulates activity',
MECHANISM='binding', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='10548111', DIRECT='YES', NOTES='',
ANNOTATOR='amattioni', SENTENCE='', SIGNOR_ID='SIGNOR-71954')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert not af.is_active
def test_signor_complexes():
test_row = _SignorRow_(ENTITYA='NFY',
TYPEA='complex',
IDA='SIGNOR-C1',
DATABASEA='SIGNOR',
ENTITYB='ID1',
TYPEB='protein',
IDB='P41134',
DATABASEB='UNIPROT',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional activation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0000972',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='18025157',
DIRECT='NO',
NOTES='',
ANNOTATOR='',
SENTENCE='',
SIGNOR_ID='SIGNOR-255746')
complex_map = {'SIGNOR-C1': ['P23511', 'P25208', 'Q13952']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 2
s0 = sp.statements[0]
assert isinstance(s0, IncreaseAmount)
assert s0.subj.db_refs['UP'] == 'P23511'
assert s0.subj.db_refs['HGNC'] == '7804'
assert s0.subj.name == 'NFYA'
assert s0.subj.bound_conditions[0].agent.db_refs['UP'] == 'P25208'
assert s0.subj.bound_conditions[0].agent.name == 'NFYB'
assert s0.subj.bound_conditions[0].agent.db_refs['HGNC'] == '7805'
assert s0.subj.bound_conditions[1].agent.db_refs['UP'] == 'Q13952'
assert s0.subj.bound_conditions[1].agent.name == 'NFYC'
assert s0.subj.bound_conditions[1].agent.db_refs['HGNC'] == '7806'
s1 = sp.statements[1]
assert isinstance(s1, Complex)
assert len(s1.evidence) == 1
assert s1.evidence[0].source_api == 'signor'
assert s1.evidence[0].source_id == 'SIGNOR-C1'
assert s1.evidence[0].text
correct_up_ids = set(['P23511', 'Q13952', 'P25208'])
correct_hgnc_ids = set(['7804', '7805', '7806'])
correct_names = set(['NFYA', 'NFYC', 'NFYB'])
actual_up_ids = set([m.db_refs['UP'] for m in s1.members])
actual_hgnc_ids = set([m.db_refs['HGNC'] for m in s1.members])
actual_names = set([m.name for m in s1.members])
assert actual_up_ids == correct_up_ids
assert actual_hgnc_ids == correct_hgnc_ids
assert actual_names == correct_names
def test_process_row_phos_multi_res():
test_row = _SignorRow_(ENTITYA='RAF1', TYPEA='protein', IDA='P04049',
DATABASEA='UNIPROT', ENTITYB='MAP2K2', TYPEB='protein',
IDB='P36507', DATABASEB='UNIPROT', EFFECT='up-regulates',
MECHANISM='phosphorylation', RESIDUE='Ser218;Ser222',
SEQUENCE='VSGQLIDsMANSFVG;LIDSMANsFVGTRSY', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='8157000', DIRECT='YES',
NOTES='', ANNOTATOR='gcesareni', SENTENCE='',
SIGNOR_ID='SIGNOR-36553')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 4
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].position == '218'
assert isinstance(stmts[2], Phosphorylation)
assert stmts[2].position == '222'
af = stmts[3]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 2
mc0 = af.agent.mods[0]
assert mc0.mod_type == 'phosphorylation'
assert mc0.residue == 'S'
assert mc0.position == '218'
mc1 = af.agent.mods[1]
assert mc1.mod_type == 'phosphorylation'
assert mc1.residue == 'S'
assert mc1.position == '222'
assert af.is_active == True
def test_process_row_complex_up():
test_row = _SignorRow_(ENTITYA='NONO', TYPEA='protein', IDA='Q15233',
DATABASEA='UNIPROT', ENTITYB='TOP1', TYPEB='protein', IDB='P11387',
DATABASEB='UNIPROT', EFFECT='up-regulates', MECHANISM='binding',
RESIDUE='', SEQUENCE='', TAX_ID='9606', CELL_DATA='BTO:0000017',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='9756848', DIRECT='YES', NOTES='', ANNOTATOR='miannu',
SENTENCE='', SIGNOR_ID='SIGNOR-60557')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert af.is_active
def test_process_row_chem_act():
test_row_chem_act = _SignorRow_(ENTITYA='Prostaglandin E2',
TYPEA='smallmolecule',
IDA='CID:5280360',
DATABASEA='PUBCHEM',
ENTITYB='GNG12',
TYPEB='protein',
IDB='Q9UBI6',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='chemical activation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='16293724',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-141820')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_act)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Activation)
def test_process_row_dephos_nores_down():
test_row = _SignorRow_(ENTITYA='CSNK1D', TYPEA='protein', IDA='P48730',
DATABASEA='UNIPROT', ENTITYB='LEF1', TYPEB='protein', IDB='Q9UJU2',
DATABASEB='UNIPROT', EFFECT='down-regulates',
MECHANISM='dephosphorylation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='15747065', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-134494')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == True
def test_process_row_dephos_down():
test_row = _SignorRow_(ENTITYA='PRKCD', TYPEA='protein', IDA='Q05655',
DATABASEA='UNIPROT', ENTITYB='PTPN22', TYPEB='protein',
IDB='Q9Y2R2', DATABASEB='UNIPROT', EFFECT='down-regulates',
MECHANISM='dephosphorylation', RESIDUE='Ser35',
SEQUENCE='FLKLKRQsTKYKADK', TAX_ID='9606', CELL_DATA='BTO:0000782',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='18056643', DIRECT='YES', NOTES='', ANNOTATOR='llicata',
SENTENCE='', SIGNOR_ID='SIGNOR-159591')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'S'
assert stmts[1].position == '35'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'S'
assert mc.position == '35'
assert af.is_active == True
def test_process_row_dephos_up():
test_row = _SignorRow_(ENTITYA='CHEK2', TYPEA='protein', IDA='O96017',
DATABASEA='UNIPROT', ENTITYB='CHEK2', TYPEB='protein', IDB='O96017',
DATABASEB='UNIPROT', EFFECT='up-regulates activity',
MECHANISM='dephosphorylation', RESIDUE='Thr387',
SEQUENCE='LMRTLCGtPTYLAPE', TAX_ID='9606', CELL_DATA='BTO:0000007',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='11901158', DIRECT='YES', NOTES='', ANNOTATOR='gcesareni',
SENTENCE='', SIGNOR_ID='SIGNOR-116131')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'T'
assert stmts[1].position == '387'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'T'
assert mc.position == '387'
assert af.is_active == False
def test_process_row_phos_multi_res():
test_row = _SignorRow_(ENTITYA='RAF1',
TYPEA='protein',
IDA='P04049',
DATABASEA='UNIPROT',
ENTITYB='MAP2K2',
TYPEB='protein',
IDB='P36507',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='phosphorylation',
RESIDUE='Ser218;Ser222',
SEQUENCE='VSGQLIDsMANSFVG;LIDSMANsFVGTRSY',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='8157000',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-36553')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 4
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].position == '218'
assert isinstance(stmts[2], Phosphorylation)
assert stmts[2].position == '222'
af = stmts[3]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 2
mc0 = af.agent.mods[0]
assert mc0.mod_type == 'phosphorylation'
assert mc0.residue == 'S'
assert mc0.position == '218'
mc1 = af.agent.mods[1]
assert mc1.mod_type == 'phosphorylation'
assert mc1.residue == 'S'
assert mc1.position == '222'
assert af.is_active == True
def test_process_row_complex_down():
test_row = _SignorRow_(ENTITYA='XIAP',
TYPEA='protein',
IDA='P98170',
DATABASEA='UNIPROT',
ENTITYB='CASP3',
TYPEB='protein',
IDB='P42574',
DATABASEB='UNIPROT',
EFFECT='down-regulates activity',
MECHANISM='binding',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='10548111',
DIRECT='YES',
NOTES='',
ANNOTATOR='amattioni',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-71954')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert not af.is_active
def test_process_row_complex_up():
test_row = _SignorRow_(ENTITYA='NONO',
TYPEA='protein',
IDA='Q15233',
DATABASEA='UNIPROT',
ENTITYB='TOP1',
TYPEB='protein',
IDB='P11387',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='binding',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0000017',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='9756848',
DIRECT='YES',
NOTES='',
ANNOTATOR='miannu',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-60557')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert af.is_active
def test_complexes_with_families():
test_row = _SignorRow_(ENTITYA='MAPK1',
TYPEA='protein',
IDA='P27361',
DATABASEA='UNIPROT',
ENTITYB='CDO/JLP/P38',
TYPEB='complex',
IDB='SIGNOR-C22',
DATABASEB='SIGNOR',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional regulation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0002314',
TISSUE_DATA='BTO:0000887;BTO:0001103',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='22863532',
DIRECT='NO',
NOTES='',
ANNOTATOR='miannu',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-198641')
complex_map = {'SIGNOR-C22': ['O60271', 'Q4KMG0', 'SIGNOR-PF14']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 2
assert isinstance(sp.statements[0], IncreaseAmount)
obj = sp.statements[0].obj
assert obj.db_refs['UP'] == 'O60271'
assert len(obj.bound_conditions) == 2
assert obj.bound_conditions[0].agent.db_refs['UP'] == 'Q4KMG0'
assert obj.bound_conditions[1].agent.db_refs['SIGNOR'] == 'SIGNOR-PF14'
assert obj.bound_conditions[1].agent.db_refs['FPLX'] == 'ROBO'
s1 = sp.statements[1]
assert isinstance(s1, Complex)
members = s1.members
assert members[0].db_refs['UP'] == 'O60271'
assert members[1].db_refs['UP'] == 'Q4KMG0'
assert members[2].db_refs['SIGNOR'] == 'SIGNOR-PF14'
assert members[2].db_refs['FPLX'] == 'ROBO'
def test_process_row_stab():
test_row_stab = _SignorRow_(ENTITYA='UCHL5', TYPEA='protein', IDA='Q9Y5K5',
DATABASEA='UNIPROT', ENTITYB='TGFBR1', TYPEB='protein',
IDB='P36897', DATABASEB='UNIPROT', EFFECT='up-regulates',
MECHANISM='stabilization', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='17052192', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-150135')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_stab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
def test_process_row_chem_act():
test_row_chem_act = _SignorRow_(ENTITYA='Prostaglandin E2',
TYPEA='smallmolecule', IDA='CID:5280360', DATABASEA='PUBCHEM',
ENTITYB='GNG12', TYPEB='protein', IDB='Q9UBI6', DATABASEB='UNIPROT',
EFFECT='up-regulates', MECHANISM='chemical activation', RESIDUE='',
SEQUENCE='', TAX_ID='9606', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='16293724', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-141820')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_act)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Activation)
def test_process_row_dephos_nores_down():
test_row = _SignorRow_(ENTITYA='CSNK1D',
TYPEA='protein',
IDA='P48730',
DATABASEA='UNIPROT',
ENTITYB='LEF1',
TYPEB='protein',
IDB='Q9UJU2',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='dephosphorylation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='15747065',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-134494')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == True
def test_process_row_dephos_nores_up():
test_row = _SignorRow_(ENTITYA='STK11',
TYPEA='protein',
IDA='Q15831',
DATABASEA='UNIPROT',
ENTITYB='AMPK',
TYPEB='complex',
IDB='SIGNOR-C15',
DATABASEB='SIGNOR',
EFFECT='up-regulates activity',
MECHANISM='dephosphorylation',
RESIDUE='',
SEQUENCE='',
TAX_ID='-1',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='14976552',
DIRECT='YES',
NOTES='',
ANNOTATOR='lperfetto',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-242602')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == False
def test_process_row_dephos_down():
test_row = _SignorRow_(ENTITYA='PRKCD',
TYPEA='protein',
IDA='Q05655',
DATABASEA='UNIPROT',
ENTITYB='PTPN22',
TYPEB='protein',
IDB='Q9Y2R2',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='dephosphorylation',
RESIDUE='Ser35',
SEQUENCE='FLKLKRQsTKYKADK',
TAX_ID='9606',
CELL_DATA='BTO:0000782',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='18056643',
DIRECT='YES',
NOTES='',
ANNOTATOR='llicata',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-159591')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'S'
assert stmts[1].position == '35'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'S'
assert mc.position == '35'
assert af.is_active == True
def test_process_row_dephos_up():
test_row = _SignorRow_(ENTITYA='CHEK2',
TYPEA='protein',
IDA='O96017',
DATABASEA='UNIPROT',
ENTITYB='CHEK2',
TYPEB='protein',
IDB='O96017',
DATABASEB='UNIPROT',
EFFECT='up-regulates activity',
MECHANISM='dephosphorylation',
RESIDUE='Thr387',
SEQUENCE='LMRTLCGtPTYLAPE',
TAX_ID='9606',
CELL_DATA='BTO:0000007',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='11901158',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-116131')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'T'
assert stmts[1].position == '387'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'T'
assert mc.position == '387'
assert af.is_active == False
def test_process_row_binding_complex():
test_row = _SignorRow_(ENTITYA='ATG5', TYPEA='protein', IDA='Q9H1Y0',
DATABASEA='UNIPROT', ENTITYB='ATG12/5/16L1', TYPEB='complex',
IDB='SIGNOR-C109', DATABASEB='SIGNOR', EFFECT='form complex',
MECHANISM='binding', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='BTO:0000007', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='18321988', DIRECT='YES', NOTES='',
ANNOTATOR='lperfetto', SENTENCE='', SIGNOR_ID='SIGNOR-226693')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Complex)
assert len(stmts[0].agent_list()) == 2
def test_process_row_chem_inh():
test_row_chem_inh = _SignorRow_(ENTITYA='722544-51-6', TYPEA='chemical',
IDA='CID:16007391', DATABASEA='PUBCHEM', ENTITYB='AURKB',
TYPEB='protein', IDB='Q96GD4', DATABASEB='UNIPROT',
EFFECT='down-regulates', MECHANISM='chemical inhibition', RESIDUE='',
SEQUENCE='', TAX_ID='9606', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='Other', DIRECT='YES',
NOTES='Selleck', ANNOTATOR='gcesareni', SENTENCE='',
SIGNOR_ID='SIGNOR-190245')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_inh)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Inhibition)
def test_process_row_destab():
test_row_destab = _SignorRow_(ENTITYA='INS', TYPEA='protein', IDA='P01308',
DATABASEA='UNIPROT', ENTITYB='APOB', TYPEB='protein', IDB='P04114',
DATABASEB='UNIPROT',
EFFECT='down-regulates quantity by destabilization',
MECHANISM='destabilization', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0000575', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='',
MODASEQ='', MODIFICATIONB='', MODBSEQ='', PMID='23721961',
DIRECT='NO', NOTES='', ANNOTATOR='miannu',
SENTENCE='', SIGNOR_ID='SIGNOR-252114')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_destab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], DecreaseAmount)
def test_mod_unknown_effect():
test_row = _SignorRow_(ENTITYA='JAK2', TYPEA='protein', IDA='O60674',
DATABASEA='UNIPROT', ENTITYB='JAK2', TYPEB='protein', IDB='O60674',
DATABASEB='UNIPROT', EFFECT='unknown', MECHANISM='phosphorylation',
RESIDUE='Tyr1007', SEQUENCE='VLPQDKEyYKVKEPG', TAX_ID='-1',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='9111318', DIRECT='YES', NOTES='', ANNOTATOR='',
SENTENCE='', SIGNOR_ID='SIGNOR-251358')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Phosphorylation)
assert stmts[0].residue == 'Y'
assert stmts[0].position == '1007'
def test_signor_family_famplex_mapping():
test_row = _SignorRow_(ENTITYA='TLRs', TYPEA='proteinfamily',
IDA='SIGNOR-PF20', DATABASEA='SIGNOR',
ENTITYB='Interferon Production', TYPEB='phenotype',
IDB='SIGNOR-PH16', DATABASEB='SIGNOR', EFFECT='up-regulates',
MECHANISM='', RESIDUE='', SEQUENCE='', TAX_ID='9606', CELL_DATA='',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='20404851', DIRECT='NO', NOTES='', ANNOTATOR='lperfetto',
SENTENCE='', SIGNOR_ID='SIGNOR-216310')
complex_map = {}
sp = SignorProcessor([test_row], complex_map)
statements = sp.statements
assert len(statements) == 1
s0 = statements[0]
assert s0.subj.db_refs['FPLX'] == 'TLR'
assert s0.subj.db_refs['SIGNOR'] == 'SIGNOR-PF20'
assert s0.subj.name == 'TLR'
def test_recursive_complexes():
test_row = _SignorRow_(ENTITYA='PAX7/MLL2 complex', TYPEA='complex',
IDA='SIGNOR-C91', DATABASEA='SIGNOR', ENTITYB='MYF5',
TYPEB='protein', IDB='P13349', DATABASEB='UNIPROT',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional regulation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0002314',
TISSUE_DATA='BTO:0000887;BTO:0001103', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='22863532', DIRECT='NO', NOTES='',
ANNOTATOR='miannu', SENTENCE='', SIGNOR_ID='SIGNOR-198641')
complex_map = {
'SIGNOR-C87': ['P61964', 'Q9UBL3', 'Q9C005', 'Q15291'],
'SIGNOR-C88': ['SIGNOR-C87', 'O14686'],
'SIGNOR-C91': ['SIGNOR-C88', 'P23759']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 4
s0 = sp.statements[0]
assert isinstance(s0, IncreaseAmount)
bc = s0.subj.bound_conditions
assert bc[0].agent.db_refs['UP'] == 'O14686'
assert bc[1].agent.db_refs['UP'] == 'P61964'
assert bc[2].agent.db_refs['UP'] == 'Q9UBL3'
assert bc[3].agent.db_refs['UP'] == 'Q9C005'
assert bc[4].agent.db_refs['UP'] == 'Q15291'
assert isinstance(sp.statements[1], Complex)
correct_complex_ups_1 = {'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'}
actual_complex_ups_1 = {m.db_refs['UP'] for m in sp.statements[1].members}
assert correct_complex_ups_1 == actual_complex_ups_1
assert isinstance(sp.statements[2], Complex)
correct_complex_ups_2 = {'O14686', 'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'}
actual_complex_ups_2 = {m.db_refs['UP'] for m in sp.statements[2].members}
assert correct_complex_ups_2 == actual_complex_ups_2
assert isinstance(sp.statements[3], Complex)
correct_complex_ups_3 = {'P23759', 'O14686', 'P61964', 'Q9UBL3', 'Q9C005',
'Q15291'}
actual_complex_ups_3 = {m.db_refs['UP'] for m in sp.statements[3].members}
assert correct_complex_ups_3 == actual_complex_ups_3
def test_signor_complexes():
test_row = _SignorRow_(ENTITYA='NFY',
TYPEA='complex', IDA='SIGNOR-C1', DATABASEA='SIGNOR', ENTITYB='ID1',
TYPEB='protein', IDB='P41134', DATABASEB='UNIPROT',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional activation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0000972', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='18025157', DIRECT='NO', NOTES='',
ANNOTATOR='', SENTENCE='', SIGNOR_ID='SIGNOR-255746')
complex_map = {'SIGNOR-C1': ['P23511', 'P25208', 'Q13952']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 2
s0 = sp.statements[0]
assert isinstance(s0, IncreaseAmount)
assert s0.subj.db_refs['UP'] == 'P23511'
assert s0.subj.db_refs['HGNC'] == '7804'
assert s0.subj.name == 'NFYA'
assert s0.subj.bound_conditions[0].agent.db_refs['UP'] == 'P25208'
assert s0.subj.bound_conditions[0].agent.name == 'NFYB'
assert s0.subj.bound_conditions[0].agent.db_refs['HGNC'] == '7805'
assert s0.subj.bound_conditions[1].agent.db_refs['UP'] == 'Q13952'
assert s0.subj.bound_conditions[1].agent.name == 'NFYC'
assert s0.subj.bound_conditions[1].agent.db_refs['HGNC'] == '7806'
s1 = sp.statements[1]
assert isinstance(s1, Complex)
assert len(s1.evidence) == 1
assert s1.evidence[0].source_api == 'signor'
assert s1.evidence[0].source_id == 'SIGNOR-C1'
assert s1.evidence[0].text
correct_up_ids = set(['P23511', 'Q13952', 'P25208'])
correct_hgnc_ids = set(['7804', '7805', '7806'])
correct_names = set(['NFYA', 'NFYC', 'NFYB'])
actual_up_ids = set([m.db_refs['UP'] for m in s1.members])
actual_hgnc_ids = set([m.db_refs['HGNC'] for m in s1.members])
actual_names = set([m.name for m in s1.members])
assert actual_up_ids == correct_up_ids
assert actual_hgnc_ids == correct_hgnc_ids
assert actual_names == correct_names
def test_mod_unknown_effect():
test_row = _SignorRow_(ENTITYA='JAK2',
TYPEA='protein',
IDA='O60674',
DATABASEA='UNIPROT',
ENTITYB='JAK2',
TYPEB='protein',
IDB='O60674',
DATABASEB='UNIPROT',
EFFECT='unknown',
MECHANISM='phosphorylation',
RESIDUE='Tyr1007',
SEQUENCE='VLPQDKEyYKVKEPG',
TAX_ID='-1',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='9111318',
DIRECT='YES',
NOTES='',
ANNOTATOR='',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-251358')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Phosphorylation)
assert stmts[0].residue == 'Y'
assert stmts[0].position == '1007'
def test_process_row_binding_complex():
test_row = _SignorRow_(ENTITYA='ATG5',
TYPEA='protein',
IDA='Q9H1Y0',
DATABASEA='UNIPROT',
ENTITYB='ATG12/5/16L1',
TYPEB='complex',
IDB='SIGNOR-C109',
DATABASEB='SIGNOR',
EFFECT='form complex',
MECHANISM='binding',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='BTO:0000007',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='18321988',
DIRECT='YES',
NOTES='',
ANNOTATOR='lperfetto',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-226693')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Complex)
assert len(stmts[0].agent_list()) == 2
def test_process_row_destab():
test_row_destab = _SignorRow_(
ENTITYA='INS',
TYPEA='protein',
IDA='P01308',
DATABASEA='UNIPROT',
ENTITYB='APOB',
TYPEB='protein',
IDB='P04114',
DATABASEB='UNIPROT',
EFFECT='down-regulates quantity by destabilization',
MECHANISM='destabilization',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0000575',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='23721961',
DIRECT='NO',
NOTES='',
ANNOTATOR='miannu',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-252114')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_destab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], DecreaseAmount)
def test_signor_family_famplex_mapping():
test_row = _SignorRow_(ENTITYA='TLRs',
TYPEA='proteinfamily',
IDA='SIGNOR-PF20',
DATABASEA='SIGNOR',
ENTITYB='Interferon Production',
TYPEB='phenotype',
IDB='SIGNOR-PH16',
DATABASEB='SIGNOR',
EFFECT='up-regulates',
MECHANISM='',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='20404851',
DIRECT='NO',
NOTES='',
ANNOTATOR='lperfetto',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-216310')
complex_map = {}
sp = SignorProcessor([test_row], complex_map)
statements = sp.statements
assert len(statements) == 1
s0 = statements[0]
assert s0.subj.db_refs['FPLX'] == 'TLR'
assert s0.subj.db_refs['SIGNOR'] == 'SIGNOR-PF20'
assert s0.subj.name == 'TLR'
from nose.plugins.attrib import attr
from indra.statements import *
from indra.databases import hgnc_client
from indra.sources.signor.processor import SignorProcessor, \
_parse_residue_positions
from indra.sources.signor.api import _SignorRow_, process_from_file, \
process_from_web
test_row = _SignorRow_(ENTITYA='RELA', TYPEA='protein', IDA='Q04206',
DATABASEA='UNIPROT', ENTITYB='MET', TYPEB='protein', IDB='P08581',
DATABASEB='UNIPROT', EFFECT='up-regulates quantity',
MECHANISM='transcriptional regulation', RESIDUE='', SEQUENCE='',
TAX_ID='10090', CELL_DATA='BTO:0002895', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='19530226', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni',
SENTENCE="Together, these results indicate that the Met gene is a "\
"direct target of NFkappaB and that Met participates "\
"in NFkappaB-mediated cell survival.",
SCORE='0.5',
SIGNOR_ID='SIGNOR-241929')
test_data_file = join(dirname(__file__), 'signor_test_data.csv')
test_complexes_file = join(dirname(__file__), 'signor_test_complexes.csv')
def test_parse_csv_from_file():
# Should work with both data file and complexes
sp = process_from_file(test_data_file, test_complexes_file, delimiter=';')
assert isinstance(sp._data, list)
from nose.tools import raises
from nose.plugins.attrib import attr
from indra.statements import *
from indra.databases import hgnc_client
from indra.sources.signor.processor import SignorProcessor, \
_parse_residue_positions
from indra.sources.signor.api import _SignorRow_, process_from_file, \
process_from_web
test_row = _SignorRow_(ENTITYA='RELA', TYPEA='protein', IDA='Q04206',
DATABASEA='UNIPROT', ENTITYB='MET', TYPEB='protein', IDB='P08581',
DATABASEB='UNIPROT', EFFECT='up-regulates quantity',
MECHANISM='transcriptional regulation', RESIDUE='', SEQUENCE='',
TAX_ID='10090', CELL_DATA='BTO:0002895', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='19530226', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni',
SENTENCE="Together, these results indicate that the Met gene is a "\
"direct target of NFkappaB and that Met participates "\
"in NFkappaB-mediated cell survival.",
SIGNOR_ID='SIGNOR-241929')
test_data_file = join(dirname(__file__), 'signor_test_data.csv')
test_complexes_file = join(dirname(__file__), 'signor_test_complexes.csv')
def test_parse_csv_from_file():
# Should work with both data file and complexes
sp = process_from_file(test_data_file, test_complexes_file)
assert isinstance(sp._data, list)
def test_recursive_complexes():
test_row = _SignorRow_(ENTITYA='PAX7/MLL2 complex',
TYPEA='complex',
IDA='SIGNOR-C91',
DATABASEA='SIGNOR',
ENTITYB='MYF5',
TYPEB='protein',
IDB='P13349',
DATABASEB='UNIPROT',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional regulation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0002314',
TISSUE_DATA='BTO:0000887;BTO:0001103',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='22863532',
DIRECT='NO',
NOTES='',
ANNOTATOR='miannu',
SENTENCE='',
SCORE='0.5',
SIGNOR_ID='SIGNOR-198641')
complex_map = {
'SIGNOR-C87': ['P61964', 'Q9UBL3', 'Q9C005', 'Q15291'],
'SIGNOR-C88': ['SIGNOR-C87', 'O14686'],
'SIGNOR-C91': ['SIGNOR-C88', 'P23759']
}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 4
s0 = sp.statements[0]
assert isinstance(s0, IncreaseAmount)
bc = s0.subj.bound_conditions
assert bc[0].agent.db_refs['UP'] == 'O14686'
assert bc[1].agent.db_refs['UP'] == 'P61964'
assert bc[2].agent.db_refs['UP'] == 'Q9UBL3'
assert bc[3].agent.db_refs['UP'] == 'Q9C005'
assert bc[4].agent.db_refs['UP'] == 'Q15291'
assert isinstance(sp.statements[1], Complex)
correct_complex_ups_1 = {'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'}
actual_complex_ups_1 = {m.db_refs['UP'] for m in sp.statements[1].members}
assert correct_complex_ups_1 == actual_complex_ups_1
assert isinstance(sp.statements[2], Complex)
correct_complex_ups_2 = {'O14686', 'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'}
actual_complex_ups_2 = {m.db_refs['UP'] for m in sp.statements[2].members}
assert correct_complex_ups_2 == actual_complex_ups_2
assert isinstance(sp.statements[3], Complex)
correct_complex_ups_3 = {
'P23759', 'O14686', 'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'
}
actual_complex_ups_3 = {m.db_refs['UP'] for m in sp.statements[3].members}
assert correct_complex_ups_3 == actual_complex_ups_3
