def test_multiple_variants(self):
node_data = Gene('HGNC',
'AKT1',
variants=[Hgvs('p.Phe508del'),
Hgvs('p.Phe509del')])
node_parent_data = node_data.get_parent()
node_parent_tuple = node_parent_data
self.graph.add_node_from_data(node_data)
self.assertIn(node_data, self.graph)
self.assertIn(node_parent_tuple, self.graph)
self.assertEqual(2, self.graph.number_of_nodes())
self.assertEqual(1, self.graph.number_of_edges())
def test_trunc_2(self):
"""Test a truncation in which the amino acid is specified."""
statement = 'trunc(Gly40)'
result = self.parser.parseString(statement)
expected = Hgvs('p.Gly40*')
self.assertEqual(expected, result.asDict())
def test_single_variant(self):
node_data = Gene('HGNC', 'AKT1', variants=Hgvs('p.Phe508del'))
node_parent_data = node_data.get_parent()
self.graph.add_node_from_data(node_data)
self.assertIn(node_data, self.graph)
self.assertIn(node_parent_data, self.graph)
self.assertEqual(2, self.graph.number_of_nodes())
self.assertEqual(1, self.graph.number_of_edges())
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_trunc_1(self):
statement = 'trunc(40)'
result = self.parser.parseString(statement)
expected = Hgvs('p.40*')
self.assertEqual(expected, result.asDict())
def test_chromosome_1(self):
statement = 'variant(g.117199646_117199648delCTT)'
expected = Hgvs('g.117199646_117199648delCTT')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
def test_chromosome_2(self):
statement = 'var(c.1521_1523delCTT)'
expected = Hgvs('c.1521_1523delCTT')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
def test_unspecified(self):
statement = 'var(=)'
expected = Hgvs('=')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
def test_frameshift(self):
statement = 'variant(p.Thr1220Lysfs)'
expected = Hgvs('p.Thr1220Lysfs')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
def test_protein_del_quoted(self):
statement = 'variant("p.Phe508del")'
expected = Hgvs('p.Phe508del')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
def test_protein_mut(self):
statement = 'var(p.Gly576Ala)'
expected = Hgvs('p.Gly576Ala')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
def test_multiple_variants(self, mock):
node_data = Gene(namespace='HGNC',
name='AKT1',
variants=[Hgvs('p.Phe508del'),
Hgvs('p.Phe509del')])
self._help_reconstitute(node_data, 2, 1)
def test_Hgvs(self, mock):
node_data = Gene(namespace='HGNC',
name='AKT1',
variants=Hgvs('p.Phe508del'))
self._help_reconstitute(node_data, 2, 1)
def test_gsub(self):
statement = 'sub(G,308,A)'
result = self.parser.parseString(statement)
expected_dict = Hgvs('c.308G>A')
self.assertEqual(expected_dict, result.asDict())
def test_psub_2(self):
statement = 'sub(Ala, 127, Tyr)'
result = self.parser.parseString(statement)
expected_list = Hgvs('p.Ala127Tyr')
self.assertEqual(expected_list, result.asDict())
def test_protein_trunc_legacy(self):
statement = 'var(p.65*)'
result = self.parser.parseString(statement)
expected = Hgvs('p.65*')
self.assertEqual(expected, result.asDict())
def test_rna_del(self):
statement = 'var(r.1653_1655delcuu)'
expected = Hgvs('r.1653_1655delcuu')
result = self.parser.parseString(statement)
self.assertEqual(expected, result.asDict())
egfr = hgnc(name='EGFR')
fadd = hgnc(name='FADD')
casp8 = hgnc(name='CASP8')
mia = hgnc(name='MIA')
il6 = Protein('HGNC', 'IL6')
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,