def test_indexing(self):
def subindex_length(x):
return (
len(x.keys()),
len(x._indicies.keys()),
len(x._names.keys())
)
self.assertEqual(
subindex_length(Gene),
(0, 0, 0)
)
_ = Gene(hgncid=1, symbol='EZH1')
self.assertEqual(
subindex_length(Gene),
(1, 1, 1)
)
_ = Gene(hgncid=2, symbol='EZH2')
self.assertEqual(
subindex_length(Gene),
(2, 2, 2)
)
Gene.clear()
self.assertEqual(
subindex_length(Gene),
(0, 0, 0)
)
def _parse_phenotype_to_gene_file(path: str) -> None:
filename = os.path.join(path, FILENAME)
with open(filename) as fh:
reader = csv.reader(remove_outcommented_rows(fh), delimiter='\t')
for cols in reader:
gene = Gene(hgncid=int(cols[HGNC_ID]), symbol=cols[GENE_SYMBOL])
gene.hpo.add(id_from_string(cols[HPO_ID]))
def test_get_gene(self):
g1 = Gene(hgncid=1, symbol='EZH1')
g2 = Gene(hgncid=2, symbol='EZH2')
self.assertEqual(Gene.get(1), g1)
self.assertEqual(Gene.get(2), g2)
self.assertEqual(Gene.get('1'), g1)
self.assertEqual(Gene.get('EZH1'), g1)
self.assertEqual(Gene.get('EZH2'), g2)
self.assertRaises(
KeyError,
lambda: Gene.get('GBA')
)
self.assertRaises(
KeyError,
lambda: Gene.get(12)
)
def test_json(self):
g = Gene(hgncid=1, symbol='Foo')
self.assertEqual(
g.toJSON(),
{'id': 1, 'name': 'Foo', 'symbol': 'Foo'}
)
self.assertEqual(
g.toJSON(verbose=True),
{'id': 1, 'name': 'Foo', 'symbol': 'Foo', 'hpo': set()}
)
def test_gene_building(self):
a = Gene(hgncid=1, symbol='EZH2')
self.assertEqual(
a.name,
'EZH2'
)
self.assertEqual(
a.id,
1
)
self.assertEqual(
a.symbol,
'EZH2'
)
self.assertEqual(
a.hpo,
set()
)
def test_singleton_handling(self):
a = Gene(hgncid=1, symbol='EZH2')
# When no name is given, ID is used for comparison
b = Gene(hgncid=1, symbol=None)
# EZH1 does not exist, but ID is used for comparison
c = Gene(hgncid=1, symbol='EZH1')
# EZH2 exists, is used for comparison
d = Gene(hgncid=2, symbol='EZH2')
# EZH2 exists, is used for comparison
e = Gene(hgncid=None, symbol='EZH2')
# EZH1 does not exist. ID does not exist => New Gene
f = Gene(hgncid=2, symbol='EZH1')
# ID is used for comparison
g = Gene(hgncid=2, symbol='EZH2')
# EZH1 is used for comparison
h = Gene(hgncid=1, symbol='EZH1')
# EZH1 is used for comparison
i = Gene(hgncid=None, symbol='EZH1')
self.assertIs(a, b)
self.assertIs(a, c)
self.assertIs(a, d)
self.assertIs(a, e)
self.assertIsNot(a, f)
self.assertIs(a, g)
self.assertIsNot(a, h)
self.assertIs(f, h)
self.assertIs(f, i)
self.assertEqual(a, b)
self.assertEqual(a, c)
self.assertEqual(a, d)
self.assertEqual(a, e)
self.assertEqual(a, g)
self.assertEqual(b, c)
self.assertEqual(b, d)
self.assertEqual(b, e)
self.assertEqual(b, g)
self.assertEqual(c, d)
self.assertEqual(c, e)
self.assertEqual(c, g)
self.assertEqual(d, e)
self.assertEqual(d, g)
self.assertEqual(e, g)
self.assertNotEqual(a, f)
self.assertNotEqual(a, h)
self.assertNotEqual(a, i)
self.assertNotEqual(b, f)
self.assertNotEqual(b, h)
self.assertNotEqual(b, i)
self.assertNotEqual(c, f)
self.assertNotEqual(c, h)
self.assertNotEqual(c, i)
self.assertNotEqual(d, f)
self.assertNotEqual(d, h)
self.assertNotEqual(d, i)
self.assertNotEqual(e, f)
self.assertNotEqual(e, h)
self.assertNotEqual(e, i)
self.assertEqual(f, h)
self.assertEqual(f, i)
self.assertEqual(h, i)
self.assertEqual(
len(Gene.keys()),
2
)
self.assertEqual(
len(Gene.values()),
2
)
self.assertEqual(
len(set(Gene.values())),
2
)
def test_string_representation(self):
g = Gene(hgncid=1, symbol='Foo')
self.assertEqual(str(g), 'Foo')
def test_equality(self):
g = Gene(hgncid=1, symbol='Foo')
self.assertEqual(g, 1)
self.assertEqual(g, 'Foo')
def make_genes(n) -> List[pyhpo.annotations.GeneSingleton]:
# Ensure to remove all items from Gene object
Gene.clear()
return [Gene(hgncid=i, symbol='Gene{}'.format(i)) for i in range(n)]