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(protein_substitution('Val', 600, 'Glu')))
self.assertEqual('pmod(Ph)', str(pmod('Ph')))
self.assertEqual('pmod(TEST:Ph)', str(pmod('Ph', namespace='TEST')))
self.assertEqual('pmod(TEST:Ph, Ser)',
str(pmod('Ph', namespace='TEST', code='Ser')))
self.assertEqual(
'pmod(TEST:Ph, Ser, 5)',
str(pmod('Ph', namespace='TEST', code='Ser', position=5)))
self.assertEqual(
'pmod(GO:"protein phosphorylation", Thr, 308)',
str(
pmod(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(Me)', str(gmod('Me')))
self.assertEqual('gmod(TEST:Me)', str(gmod('Me', namespace='TEST')))
self.assertEqual('gmod(GO:"DNA Methylation")',
str(gmod('DNA Methylation', namespace='GO')))
def test_fragments(self):
self.assertTrue(
has_fragment(
protein(name='APP',
namespace='HGNC',
variants=[
fragment(start=672,
stop=713,
description='random text')
])))
self.assertTrue(
has_fragment(
protein(name='APP', namespace='HGNC', variants=[fragment()])))
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_convert_fragments(self):
"""Test the conversion of a bel statement like A -> p(B, frag(?))."""
casp3 = abundance('HGNC', 'CASP3', 'MeSH:D017628')
tau = protein('HGNC', 'MAPT', 'HGNC:6893', variants=fragment())
# act(p(HGNC:CASP3), ma(pep)) increases p(HGNC:MAPT, frag("?"))
bel_graph = BELGraph()
bel_graph.add_increases(casp3,
tau,
evidence='10.1038/s41586-018-0368-8',
citation='PubMed:30046111')
expected_reified_graph = self.help_make_simple_expected_graph(
casp3, tau, FRAGMENTS, 0, self.help_causal_increases)
reified_graph = reify_bel_graph(bel_graph)
self.help_test_graphs_equal(expected_reified_graph, reified_graph)
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())
is_protein,
is_translocated,
keep_node_permissive,
node_exclusion_predicate_builder,
node_inclusion_predicate_builder,
not_pathology,
)
from pybel.testing.utils import n
p1 = protein(name='BRAF', namespace='HGNC')
p2 = protein(name='BRAF',
namespace='HGNC',
variants=[hgvs('p.Val600Glu'), pmod('Ph')])
p3 = protein(name='APP',
namespace='HGNC',
variants=fragment(start=672, stop=713))
p4 = protein(name='2', namespace='HGNC')
g1 = gene(name='BRAF', namespace='HGNC', variants=gmod('Me'))
class TestNodePredicates(unittest.TestCase):
"""Tests for node predicates."""
def test_none_data(self):
"""Test permissive node predicate with a node data dictionary."""
self.assertTrue(keep_node_permissive(p1))
def test_none(self):
"""Test permissive node predicate with graph and tuple."""
g = BELGraph()
p1_tuple = g.add_node_from_data(p1)
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))
from pybel.struct.filters.edge_predicate_builders import build_relation_predicate
from pybel.struct.filters.edge_predicates import (
edge_has_activity, edge_has_annotation, edge_has_degradation,
edge_has_translocation, has_authors, has_polarity, has_provenance, has_pubmed, is_associative_relation,
is_causal_relation, is_direct_causal_relation,
)
from pybel.struct.filters.node_predicates import (
has_activity, has_causal_in_edges, has_causal_out_edges, has_fragment, has_gene_modification, has_hgvs,
has_protein_modification, has_variant, is_abundance, is_causal_central, is_causal_sink, is_causal_source,
is_degraded, is_gene, is_pathology, is_protein, is_translocated, none_of, not_pathology, one_of,
)
from pybel.testing.utils import n
p1 = protein(name='BRAF', namespace='HGNC')
p2 = protein(name='BRAF', namespace='HGNC', variants=[hgvs('p.Val600Glu'), pmod('Ph')])
p3 = protein(name='APP', namespace='HGNC', variants=fragment(start=672, stop=713))
p4 = protein(name='2', namespace='HGNC')
g1 = gene(name='BRAF', namespace='HGNC', variants=gmod('Me'))
class TestNodePredicates(unittest.TestCase):
"""Tests for node predicates."""
def test_none_data(self):
"""Test permissive node predicate with a node data dictionary."""
self.assertTrue(true_node_predicate(p1))
self.assertFalse(false_node_predicate(p1))
def test_none(self):
"""Test permissive node predicate with graph and tuple."""
