def count_variants(graph):
"""Counts how many of each type of variant a graph has
:param pybel.BELGraph graph: A BEL graph
:rtype: Counter
"""
return Counter(variant_data[KIND]
for node, data in graph.iter_node_data_pairs()
if has_variant(graph, node)
for variant_data in data[VARIANTS])
def test_g1_variants(self):
self.assertFalse(is_abundance(g1))
self.assertTrue(is_gene(g1))
self.assertFalse(is_protein(g1))
self.assertFalse(is_pathology(g1))
self.assertTrue(has_variant(g1))
self.assertTrue(has_gene_modification(g1), msg='Should have {}: {}'.format(GMOD, g1))
self.assertFalse(has_protein_modification(g1))
self.assertFalse(has_hgvs(g1))
def test_p2_data_variants(self):
self.assertFalse(is_abundance(p2))
self.assertFalse(is_gene(p2))
self.assertTrue(is_protein(p2))
self.assertFalse(is_pathology(p2))
self.assertTrue(not_pathology(p2))
self.assertTrue(has_variant(p2))
self.assertFalse(has_gene_modification(p2))
self.assertTrue(has_protein_modification(p2))
self.assertTrue(has_hgvs(p2))
def test_p3(self):
self.assertFalse(is_abundance(p3))
self.assertFalse(is_gene(p3))
self.assertTrue(is_protein(p3))
self.assertFalse(is_pathology(p3))
self.assertTrue(not_pathology(p3))
self.assertTrue(has_variant(p3))
self.assertFalse(has_gene_modification(p3))
self.assertFalse(has_protein_modification(p3))
self.assertFalse(has_hgvs(p3))
self.assertTrue(has_fragment(p3))
def test_p1_data_variants(self):
"""Test node predicates on BRAF."""
self.assertFalse(is_abundance(p1))
self.assertFalse(is_gene(p1))
self.assertTrue(is_protein(p1))
self.assertFalse(is_pathology(p1))
self.assertTrue(not_pathology(p1))
self.assertFalse(has_variant(p1))
self.assertFalse(has_protein_modification(p1))
self.assertFalse(has_gene_modification(p1))
self.assertFalse(has_hgvs(p1))
self.assertFalse(has_fragment(p1))
def test_p2_tuple_variants(self):
g = BELGraph()
g.add_node_from_data(p2)
self.assertFalse(is_abundance(g, p2))
self.assertFalse(is_gene(g, p2))
self.assertTrue(is_protein(g, p2))
self.assertFalse(is_pathology(g, p2))
self.assertTrue(not_pathology(g, p2))
self.assertTrue(has_variant(g, p2))
self.assertFalse(has_gene_modification(g, p2))
self.assertTrue(has_protein_modification(g, p2))
self.assertTrue(has_hgvs(g, p2))
def test_p1_tuple_variants(self):
"""Test node predicates on the node tuple from BRAF.s"""
g = BELGraph()
g.add_node_from_data(p1)
self.assertFalse(is_abundance(g, p1))
self.assertFalse(is_gene(g, p1))
self.assertTrue(is_protein(g, p1))
self.assertFalse(is_pathology(g, p1))
self.assertTrue(not_pathology(g, p1))
self.assertFalse(has_variant(g, p1))
self.assertFalse(has_protein_modification(g, p1))
self.assertFalse(has_gene_modification(g, p1))
self.assertFalse(has_hgvs(g, p1))
