Python EdgeSet.get_outgoing_kmers Examples

Example #1

File: test_edge_set.py Project: winni2k/cortexpy

 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')

Example #2

File: test_edge_set.py Project: winni2k/cortexpy

 def test_outgoing_returns_lexicographically_lowest_kmers(self):
     es = EdgeSet(np.zeros(8))
     es.add_edge('G')
     assert ['CCG'] == es.get_outgoing_kmers('ACG')

Example #3

File: test_edge_set.py Project: winni2k/cortexpy

 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'))

Example #4

File: test_edge_set.py Project: winni2k/cortexpy

 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'))

Example #5

File: test_edge_set.py Project: winni2k/cortexpy

 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'))