def test_raises_on_non_lexlo_kmer(self):
es = EdgeSet(np.zeros(8))
with pytest.raises(AssertionError):
es.get_outgoing_kmers('TTT')
with pytest.raises(AssertionError):
es.get_incoming_kmers('TTT')
def test_outgoing_returns_lexicographically_lowest_kmers(self):
es = EdgeSet(np.zeros(8))
es.add_edge('G')
assert ['CCG'] == es.get_outgoing_kmers('ACG')
def test_all_incoming_no_outgoing(self):
es = EdgeSet(np.concatenate([np.ones(4), np.zeros(4)]))
assert es.get_incoming_kmers('AAA') == ['AAA', 'CAA', 'GAA', 'TAA']
assert 0 == len(es.get_outgoing_kmers('AAA'))
def test_no_incoming_all_outgoing(self):
es = EdgeSet(np.concatenate([np.zeros(4), np.ones(4)]))
assert 0 == len(es.get_incoming_kmers('AAA'))
assert {'AAA', 'AAC', 'AAG', 'AAT'} == set(es.get_outgoing_kmers('AAA'))
def test_no_incoming_or_outgoing(self):
es = EdgeSet(np.zeros(8))
assert 0 == len(es.get_incoming_kmers('AAA'))
assert 0 == len(es.get_outgoing_kmers('AAA'))