Exemple #1
0
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
Exemple #2
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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
Exemple #3
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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
Exemple #4
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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)
Exemple #5
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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)
Exemple #6
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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)
Exemple #7
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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
Exemple #8
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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)
Exemple #9
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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')
Exemple #10
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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
Exemple #11
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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
Exemple #12
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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
Exemple #13
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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
Exemple #14
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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)
Exemple #15
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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')
Exemple #16
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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'
Exemple #17
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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)
Exemple #18
0
from os.path import join, dirname
from nose.tools import raises

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)
    assert isinstance(sp._data[0], SignorRow)