def test_fragment_specified_end_only(self, mock):
dummy_namespace = n()
dummy_name = n()
node_data = Protein(namespace=dummy_namespace,
name=dummy_name,
variants=[Fragment(start='*', stop=1000)])
self._help_reconstitute(node_data, 2, 1)
def test_fragment_unspecified(self, mock):
dummy_namespace = n()
dummy_name = n()
node_data = Protein(namespace=dummy_namespace,
name=dummy_name,
variants=[Fragment()])
self._help_reconstitute(node_data, 2, 1)
def test_get_parent(self):
"""Test the get_parent function in :class:`CentralDogmaAbundance`s."""
ab42 = Protein(name='APP',
namespace='HGNC',
variants=[Fragment(start=672, stop=713)])
app = ab42.get_parent()
self.assertEqual('p(HGNC:APP)', app.as_bel())
self.assertEqual('p(HGNC:APP, frag("672_713"))', ab42.as_bel())
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 test_variants_mapping(self):
graph = BELGraph()
app = Protein(HGNC, 'APP')
app_fragment = app.with_variants(Fragment('1_49'))
graph.add_node_from_data(app_fragment)
mapped_nodes = get_mapped_nodes(graph, HGNC, {'APP'})
self.assertEqual(1, len(mapped_nodes))
self.assertIn(app, mapped_nodes)
self.assertEqual({app_fragment}, mapped_nodes[app])
def test_protein_fragment(self):
node = Protein(name='APP',
namespace='HGNC',
variants=[Fragment(start=672, stop=713)])
self.assertEqual('p(HGNC:APP, frag("672_713"))', str(node))
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,
Protein('HGNC', 'MIA', variants=Fragment(1, '?')),
Protein('HGNC', 'MIA', variants=Fragment()),
Protein('HGNC', 'MIA', variants=Fragment(description='55kD')),
Protein('HGNC', 'CFTR', variants=Hgvs('p.Gly576Ala')),
akt1_rna,
Rna('HGNC', 'AKT1', variants=[Hgvs('c.1521_1523delCTT'), Hgvs('p.Phe508del')]),
Gene('HGNC', 'NCF1'),
ComplexAbundance([
Gene('HGNC', 'NCF1'),
Protein('HGNC', 'HBP1')
]),
Protein('HGNC', 'HBP1'),
ComplexAbundance([Protein('HGNC', 'FOS'), Protein('HGNC', 'JUN')]),
def test_with_variants_list(self):
"""Test the `with_variant` function in :class:`CentralDogmaAbundance`s."""
app = Protein(name='APP', namespace='HGNC')
ab42 = app.with_variants([Fragment(start=672, stop=713)])
self.assertEqual('p(HGNC:APP)', app.as_bel())
self.assertEqual('p(HGNC:APP, frag("672_713"))', ab42.as_bel())
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,
Protein('HGNC', 'MIA', variants=Fragment(1, '?')),
Protein('HGNC', 'MIA', variants=Fragment()),
Protein('HGNC', 'MIA', variants=Fragment(description='55kD')),
Protein('HGNC', 'CFTR', variants=Hgvs('p.Gly576Ala')), akt1_rna,
Rna('HGNC',
'AKT1',
variants=[Hgvs('c.1521_1523delCTT'),
Hgvs('p.Phe508del')]),
Gene('HGNC', 'NCF1'),
ComplexAbundance([Gene('HGNC', 'NCF1'),
Protein('HGNC', 'HBP1')]),
Protein('HGNC', 'HBP1'),
ComplexAbundance([Protein('HGNC', 'FOS'),
Protein('HGNC', 'JUN')]),
Protein('HGNC', 'FOS'),
