def test_composite(self):
il23 = NamedComplexAbundance(namespace='GO',
name='interleukin-23 complex')
il6 = Protein(namespace='HGNC', name='IL6')
node_data = CompositeAbundance([il23, il6])
self.graph.add_node_from_data(node_data)
self.assertIn(node_data, self.graph)
self.assertEqual(3, self.graph.number_of_nodes())
self.assertIn(il6,
self.graph,
msg='Nodes:\n'.format('\n'.join(map(str, self.graph))))
self.assertIn(il23, self.graph)
self.assertEqual(2, self.graph.number_of_edges())
self.assertIn(node_data, self.graph[il6])
edges = list(self.graph[il6][node_data].values())
self.assertEqual(1, len(edges))
data = edges[0]
self.assertEqual(PART_OF, data[RELATION])
self.assertIn(node_data, self.graph[il23])
edges = list(self.graph[il23][node_data].values())
self.assertEqual(1, len(edges))
data = edges[0]
self.assertEqual(PART_OF, data[RELATION])
def test_composite(self, mock):
interleukin_23_complex = NamedComplexAbundance(
'GO', 'interleukin-23 complex')
il6 = hgnc(name='IL6')
interleukin_23_and_il6 = CompositeAbundance(
[interleukin_23_complex, il6])
self._help_reconstitute(interleukin_23_and_il6, 3, 2)
def as_bel(self) -> Optional[BaseEntity]:
"""Get BEL thing."""
if self.db == 'ComplexPortal':
return NamedComplexAbundance(
namespace='complexportal',
name=self.db_symbol,
identifier=self.db_id,
)
def as_bel(self) -> Optional[BaseEntity]:
"""Convert this term to a BEL node."""
if self.namespace == 'biological_process':
return gobp(
name=self.name,
identifier=self.go_id,
)
if self.namespace == 'cellular_component':
if self.is_complex:
return NamedComplexAbundance(
namespace='go',
name=self.name,
identifier=self.go_id,
)
else:
return Abundance(
namespace='go',
name=self.name,
identifier=self.go_id,
)
def node_to_bel(node: Dict, graph, hgnc_manager: HgncManager,
chebi_manager: ChebiManager, species) -> BaseEntity:
"""Convert node dictionary to BEL node object."""
node_types = node['entity_type']
identifier, name, namespace = get_valid_node_parameters(
node, hgnc_manager, chebi_manager, species)
members = set()
if namespace == 'hgnc_multiple_entry':
return composite_abundance(process_multiple_proteins(identifier))
elif 'Protein' in node_types:
return protein(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'Dna' in node_types:
return gene(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'Rna' in node_types:
return rna(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'SmallMolecule' in node_types:
return abundance(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'PhysicalEntity' in node_types:
return abundance(namespace=namespace.upper(),
name=name,
identifier=identifier)
elif 'Complex' in node_types:
complex_components = node.get('complex_components')
if complex_components:
for component in complex_components:
bel_node = node_to_bel(component, graph, hgnc_manager,
chebi_manager, species)
members.add(bel_node)
if members:
return complex_abundance(name=node.get('display_name'),
members=members,
identifier=identifier,
namespace=namespace.upper())
else:
return NamedComplexAbundance(name=node.get('display_name'),
identifier=identifier,
namespace=namespace.upper())
elif 'Pathway' in node_types:
bioprocess_node = bioprocess(identifier=identifier,
name=name,
namespace=namespace.upper())
graph.add_node_from_data(bioprocess_node)
return bioprocess_node
else:
log.warning('Entity type not recognized', node_types)
def test_named_complex_abundance(self):
node = NamedComplexAbundance(namespace='SCOMP',
name='Calcineurin Complex')
self.assertEqual('complex(SCOMP:"Calcineurin Complex")', str(node))
adgrb1 = Protein(namespace='HGNC', name='ADGRB1')
adgrb2 = Protein(namespace='HGNC', name='ADGRB2')
adgrb_complex = ComplexAbundance([adgrb1, adgrb2])
achlorhydria = Pathology(namespace='MESHD', name='Achlorhydria')
akt1_rna = akt1.get_rna()
akt1_gene = akt1_rna.get_gene()
akt_methylated = akt1_gene.with_variants(GeneModification('Me'))
akt1_phe_508_del = akt1_gene.with_variants(Hgvs('p.Phe508del'))
cftr = hgnc('CFTR')
cftr_protein_unspecified_variant = cftr.with_variants(HgvsUnspecified())
cftr_protein_phe_508_del = cftr.with_variants(Hgvs('p.Phe508del'))
adenocarcinoma = Pathology('MESHD', 'Adenocarcinoma')
interleukin_23_complex = NamedComplexAbundance('GO', 'interleukin-23 complex')
oxygen_atom = Abundance(namespace='CHEBI', name='oxygen atom')
hydrogen_peroxide = Abundance('CHEBI', 'hydrogen peroxide')
tmprss2_gene = Gene('HGNC', 'TMPRSS2')
tmprss2_erg_gene_fusion = GeneFusion(
partner_5p=tmprss2_gene,
range_5p=EnumeratedFusionRange('c', 1, 79),
partner_3p=Gene('HGNC', 'ERG'),
range_3p=EnumeratedFusionRange('c', 312, 5034)
)
bcr_jak2_gene_fusion = GeneFusion(
partner_5p=Gene('HGNC', 'BCR'),
Abundance,
BiologicalProcess,
ComplexAbundance,
NamedComplexAbundance,
Pathology,
Protein,
ProteinModification,
)
from pybel.language import activity_mapping
from pybel.testing.constants import test_jgif_path
from tests.constants import TestGraphMixin
logging.getLogger('pybel.parser').setLevel(20)
calcium = Abundance('SCHEM', 'Calcium')
calcineurin_complex = NamedComplexAbundance('SCOMP', 'Calcineurin Complex')
foxo3 = Protein('HGNC', 'FOXO3')
tcell_proliferation = BiologicalProcess(
'GO', 'CD8-positive, alpha-beta T cell proliferation')
il15 = Protein('HGNC', 'IL15')
il2rg = Protein('MGI', 'Il2rg')
jgif_expected_nodes = {
calcium,
calcineurin_complex,
foxo3,
tcell_proliferation,
il15,
il2rg,
Protein('HGNC', 'CXCR6'),
Protein('HGNC', 'IL15RA'),
BiologicalProcess('GO', 'lymphocyte chemotaxis'),
def _assoc(y):
return {RELATION: ASSOCIATION, 'association_type': y}
a1 = Abundance('CHEBI', '1')
p1 = Protein('HGNC', '1')
pf1 = Protein('INTERPRO', '1')
d1 = Pathology('MESH', '1')
b1 = BiologicalProcess('GO', '1')
b2 = BiologicalProcess('GO', '2')
m1 = MicroRna('MIRBASE', '1')
r1 = Rna('HGNC', '1')
r2 = Rna('HGNC', '2')
nca1 = NamedComplexAbundance('FPLX', '1')
pop1 = Population('taxonomy', '1')
p2 = Protein('HGNC', identifier='9236')
p3 = Protein('HGNC', identifier='9212')
r3 = p3.get_rna()
g3 = r3.get_gene()
c1 = ComplexAbundance([p2, g3])
c2 = ComplexAbundance([p1, p2])
c3 = ComplexAbundance([a1, p2])
converters_true_list = [
(PartOfNamedComplexConverter, p1, nca1, _rel(PART_OF), ('HGNC:1', 'partOf',
'FPLX:1')),
(SubprocessPartOfBiologicalProcessConverter, b1, b2, _rel(PART_OF),
adgrb1 = Protein(namespace='HGNC', name='ADGRB1')
adgrb2 = Protein(namespace='HGNC', name='ADGRB2')
adgrb_complex = ComplexAbundance([adgrb1, adgrb2])
achlorhydria = Pathology(namespace='MESHD', name='Achlorhydria')
akt1_rna = akt1.get_rna()
akt1_gene = akt1_rna.get_gene()
akt_methylated = akt1_gene.with_variants(GeneModification('Me'))
akt1_phe_508_del = akt1_gene.with_variants(Hgvs('p.Phe508del'))
cftr = hgnc(name='CFTR')
cftr_protein_unspecified_variant = cftr.with_variants(HgvsUnspecified())
cftr_protein_phe_508_del = cftr.with_variants(Hgvs('p.Phe508del'))
adenocarcinoma = Pathology('MESHD', 'Adenocarcinoma')
interleukin_23_complex = NamedComplexAbundance('GO', 'interleukin-23 complex')
oxygen_atom = Abundance(namespace='CHEBI', name='oxygen atom')
hydrogen_peroxide = Abundance('CHEBI', 'hydrogen peroxide')
tmprss2_gene = Gene('HGNC', 'TMPRSS2')
tmprss2_erg_gene_fusion = GeneFusion(
partner_5p=tmprss2_gene,
range_5p=EnumeratedFusionRange('c', 1, 79),
partner_3p=Gene('HGNC', 'ERG'),
range_3p=EnumeratedFusionRange('c', 312, 5034))
bcr_jak2_gene_fusion = GeneFusion(
partner_5p=Gene('HGNC', 'BCR'),
range_5p=EnumeratedFusionRange('c', '?', 1875),