def test_protein_pmod(self):
node = Protein(name='PLCG1',
namespace='HGNC',
variants=[ProteinModification(name='Ph', code='Tyr')])
self.assertEqual(
'p(HGNC:PLCG1, pmod(go:0006468 ! "protein phosphorylation", Tyr))',
str(node))
def test_pmod_default_with_residue(self, mock):
dummy_namespace = n()
dummy_name = n()
node_data = Protein(namespace=dummy_namespace,
name=dummy_name,
variants=[ProteinModification('Me', code='Ser')])
self._help_reconstitute(node_data, 2, 1)
def test_canonicalize_variant_dsl(self):
"""Use the __str__ functions in the DSL to create BEL instead of external pybel.canonicalize."""
self.assertEqual('var("p.Val600Glu")', str(Hgvs('p.Val600Glu')))
self.assertEqual('var("p.Val600Glu")',
str(ProteinSubstitution('Val', 600, 'Glu')))
self.assertEqual('pmod(go:0006468 ! "protein phosphorylation")',
str(ProteinModification('Ph')))
self.assertEqual('pmod(TEST:Ph)',
str(ProteinModification('Ph', namespace='TEST')))
self.assertEqual(
'pmod(TEST:Ph, Ser)',
str(ProteinModification('Ph', namespace='TEST', code='Ser')))
self.assertEqual(
'pmod(TEST:Ph, Ser, 5)',
str(
ProteinModification('Ph',
namespace='TEST',
code='Ser',
position=5)))
self.assertEqual(
'pmod(GO:"protein phosphorylation", Thr, 308)',
str(
ProteinModification(name='protein phosphorylation',
namespace='GO',
code='Thr',
position=308)))
self.assertEqual('frag("?")', str(Fragment()))
self.assertEqual('frag("672_713")', str(Fragment(start=672, stop=713)))
self.assertEqual('frag("?", "descr")',
str(Fragment(description='descr')))
self.assertEqual(
'frag("672_713", "descr")',
str(Fragment(start=672, stop=713, description='descr')))
self.assertEqual('gmod(go:0006306 ! "DNA methylation")',
str(GeneModification('Me')))
self.assertEqual('gmod(TEST:Me)',
str(GeneModification('Me', namespace='TEST')))
self.assertEqual(
'gmod(GO:"DNA Methylation")',
str(GeneModification('DNA Methylation', namespace='GO')))
def _help_test_non_standard_namespace(self, statement):
result = self.parser.parseString(statement)
expected = {
KIND: PMOD,
CONCEPT: Entity(namespace='MOD', name='PhosRes'),
PMOD_CODE: 'Ser',
PMOD_POSITION: 473,
}
self.assertEqual(expected, ProteinModification(name='PhosRes', namespace='MOD', code='Ser', position=473))
self.assertEqual(expected, result.asDict())
def _help_test_pmod_simple(self, statement):
result = self.parser.parseString(statement)
expected = {
KIND: PMOD,
CONCEPT: {
NAMESPACE: BEL_DEFAULT_NAMESPACE,
NAME: 'Ph',
},
}
self.assertEqual(expected, ProteinModification('Ph'))
self.assertEqual(expected, result.asDict())
def _help_test_pmod_simple(self, statement):
result = self.parser.parseString(statement)
expected = {
KIND: PMOD,
CONCEPT: {
NAMESPACE: 'go',
NAME: 'protein phosphorylation',
IDENTIFIER: '0006468',
},
}
self.assertEqual(expected, ProteinModification('Ph'))
self.assertEqual(expected, result.asDict())
def test_pmod_custom_simple(self, mock):
dummy_namespace = 'HGNC'
dummy_name = 'AKT1'
dummy_mod_namespace = 'GO'
dummy_mod_name = 'Protein phosphorylation'
node_data = Protein(namespace=dummy_namespace,
name=dummy_name,
variants=[
ProteinModification(
name=dummy_mod_name,
namespace=dummy_mod_namespace)
])
self._help_reconstitute(node_data, 2, 1)
def _help_test_pmod_full(self, statement):
result = self.parser.parseString(statement)
expected = {
KIND: PMOD,
CONCEPT: {
NAMESPACE: BEL_DEFAULT_NAMESPACE,
NAME: 'Ph',
},
PMOD_CODE: 'Ser',
PMOD_POSITION: 473,
}
self.assertEqual(expected, ProteinModification('Ph', code='Ser', position=473))
self.assertEqual(expected, result.asDict())
def _help_test_pmod_full(self, statement):
result = self.parser.parseString(statement)
expected = {
KIND: PMOD,
CONCEPT: {
NAMESPACE: 'go',
NAME: 'protein phosphorylation',
IDENTIFIER: '0006468',
},
PMOD_CODE: 'Ser',
PMOD_POSITION: 473,
}
self.assertEqual(expected,
ProteinModification('Ph', code='Ser', position=473))
self.assertEqual(expected, result.asDict())
akt_methylated,
bcr_jak2_rna_fusion,
chchd4_aifm1_rna_fusion,
akt1_gene,
akt1_phe_508_del,
akt1,
Gene('HGNC', 'AKT1', variants=Hgvs('c.308G>A')),
tmprss2_erg_gene_fusion,
Gene('HGNC', 'AKT1', variants=[Hgvs('c.1521_1523delCTT'), Hgvs('c.308G>A'), Hgvs('p.Phe508del')]),
MicroRna('HGNC', 'MIR21'),
bcr_jak2_gene_fusion,
Gene('HGNC', 'CFTR', variants=Hgvs('c.1521_1523delCTT')),
Gene('HGNC', 'CFTR'),
Gene('HGNC', 'CFTR', variants=Hgvs('g.117199646_117199648delCTT')),
Gene('HGNC', 'CFTR', variants=Hgvs('c.1521_1523delCTT')),
Protein('HGNC', 'AKT1', variants=ProteinModification('Ph', 'Ser', 473)),
MicroRna('HGNC', 'MIR21', variants=Hgvs('p.Phe508del')),
Protein('HGNC', 'AKT1', variants=Hgvs('p.C40*')),
Protein('HGNC', 'AKT1', variants=[Hgvs('p.Ala127Tyr'), ProteinModification('Ph', 'Ser')]),
chchd4_aifm1_gene_fusion,
tmprss2_erg_protein_fusion,
Protein('HGNC', 'AKT1', variants=Hgvs('p.Arg1851*')),
bcr_jak2_protein_fusion,
Protein('HGNC', 'AKT1', variants=Hgvs('p.40*')),
chchd4_aifm1_protein_fusion,
Protein('HGNC', 'CFTR', variants=HgvsReference()),
cftr,
egfr,
cftr_protein_unspecified_variant,
adenocarcinoma,
cftr_protein_phe_508_del,
Protein('HGNC', 'CXCR3'),
Abundance('CHEBI', 'acrolein'),
Protein('HGNC', 'IDO2'),
Pathology('MESHD', 'Pulmonary Disease, Chronic Obstructive'),
Protein('HGNC', 'IFNG'),
Protein('HGNC', 'TNFRSF4'),
Protein('HGNC', 'CTLA4'),
Protein('HGNC', 'GZMA'),
Protein('HGNC', 'PRF1'),
Protein('HGNC', 'TNF'),
Protein('SFAM', 'Chemokine Receptor Family'),
ComplexAbundance([Protein('HGNC', 'CD8A'),
Protein('HGNC', 'CD8B')]),
ComplexAbundance([Protein('HGNC', 'CD8A'),
Protein('HGNC', 'CD8B')]),
Protein('HGNC', 'PLCG1', variants=ProteinModification('Ph', 'Tyr')),
Protein('EGID', '21577'),
}
jgif_expected_edges = [
(calcium, calcineurin_complex, {
RELATION: DIRECTLY_INCREASES,
EVIDENCE:
'NMDA-mediated influx of calcium led to activated of the calcium-dependent phosphatase calcineurin and the subsequent dephosphorylation and activation of the protein-tyrosine phosphatase STEP',
CITATION: {
NAMESPACE: CITATION_TYPE_PUBMED,
IDENTIFIER: '12483215'
},
TARGET_MODIFIER: {
MODIFIER: ACTIVITY,
EFFECT: activity_mapping['phos']
pybel.dsl.activity(
name='ATPase activity',
namespace='go',
identifier='0016887',
),
'psi-mi:"MI:1146"(phospholipase reaction)':
pybel.dsl.activity(
name='phospholipase activity',
namespace='go',
identifier='0004620',
),
}
PROTEIN_INCREASES_MOD_DICT: Mapping[str, ProteinModification] = {
'psi-mi:"MI:0844"(phosphotransfer reaction)':
ProteinModification('Ph'),
'psi-mi:"MI:0559"(glycosylation reaction)':
ProteinModification('Glyco'),
'psi-mi:"MI:0216"(palmitoylation reaction)':
ProteinModification('Palm'),
'psi-mi:"MI:1327"(sulfurtransfer reaction)':
ProteinModification('Sulf'),
'psi-mi:"MI:0217"(phosphorylation reaction)':
ProteinModification('Ph'),
'psi-mi:"MI:0566"(sumoylation reaction)':
ProteinModification('Sumo'),
'psi-mi:"MI:0213"(methylation reaction)':
ProteinModification('Me'),
'psi-mi:"MI:0556"(transglutamination reaction)':
ProteinModification(
namespace='mi',
akt_methylated, bcr_jak2_rna_fusion, chchd4_aifm1_rna_fusion, akt1_gene,
akt1_phe_508_del, akt1,
Gene('HGNC', 'AKT1', variants=Hgvs('c.308G>A')), tmprss2_erg_gene_fusion,
Gene('HGNC',
'AKT1',
variants=[
Hgvs('c.1521_1523delCTT'),
Hgvs('c.308G>A'),
Hgvs('p.Phe508del')
]),
MicroRna('HGNC', 'MIR21'), bcr_jak2_gene_fusion,
Gene('HGNC', 'CFTR', variants=Hgvs('c.1521_1523delCTT')),
Gene('HGNC', 'CFTR'),
Gene('HGNC', 'CFTR', variants=Hgvs('g.117199646_117199648delCTT')),
Gene('HGNC', 'CFTR', variants=Hgvs('c.1521_1523delCTT')),
Protein('HGNC', 'AKT1', variants=ProteinModification('Ph', 'Ser', 473)),
MicroRna('HGNC', 'MIR21', variants=Hgvs('p.Phe508del')),
Protein('HGNC', 'AKT1', variants=Hgvs('p.C40*')),
Protein('HGNC',
'AKT1',
variants=[Hgvs('p.Ala127Tyr'),
ProteinModification('Ph', 'Ser')]),
chchd4_aifm1_gene_fusion, tmprss2_erg_protein_fusion,
Protein('HGNC', 'AKT1',
variants=Hgvs('p.Arg1851*')), bcr_jak2_protein_fusion,
Protein('HGNC', 'AKT1',
variants=Hgvs('p.40*')), chchd4_aifm1_protein_fusion,
Protein('HGNC', 'CFTR', variants=HgvsReference()), cftr, egfr,
cftr_protein_unspecified_variant, adenocarcinoma, cftr_protein_phe_508_del,
Protein('HGNC', 'MIA', variants=Fragment(5,
20)), mia, interleukin_23_complex,