def test_single_kmer_revcomp_seed(self, seed): # given b = get_cortex_builder() b.with_kmer('AAA 1 ......G.') b.with_kmer('AAG 1 a.......') cdb = b.build() # when graph = Interactor(cdb).make_graph_nodes_consistent([seed]).graph # then if seed == 'AAA': assert [] == list(graph.in_edges(seed)) assert [('AAA', 'AAG')] == list(graph.out_edges(seed)) else: assert [('CTT', 'TTT')] == list(graph.in_edges(seed)) assert [] == list(graph.out_edges(seed))
def test_gets_correct_neighbors_of_kmer(self): # given b = get_cortex_builder() b.with_kmer('AAC 1 .......T') b.with_kmer('ACT 1 a.....G.') b.with_kmer('CAG 1 .......T') cdb = b.build() seed = 'AAC' # when graph = Interactor(cdb).make_graph_nodes_consistent([seed]).graph # then assert ['CTG'] == list(graph['ACT']) assert ['CTG'] == list(graph.succ['ACT']) assert ['AAC'] == list(graph.pred['ACT']) assert [('ACT', 'CTG')] == list(graph.out_edges('ACT')) assert [('AAC', 'ACT')] == list(graph.in_edges('ACT')) assert [] == list(graph['CTG']) assert [] == list(graph.succ['CTG']) assert ['ACT'] == list(graph.pred['CTG']) assert [] == list(graph.out_edges('CTG')) assert [('ACT', 'CTG')] == list(graph.in_edges('CTG'))