def test_overlap_create(): kmers = ['ATGCG', 'GCATG', 'CATGC', 'AGGCA', 'GGCAT'] expected = [('GCATG', 'CATGC'), ('CATGC', 'ATGCG'), ('AGGCA', 'GGCAT'), ('GGCAT', 'GCATG')] actual = overlapgraph.create(kmers) expected.sort() actual.sort() assert (expected == actual)
import overlapgraph, sys filename = sys.argv[1] with open(filename, 'r') as f: kmers = [line.strip() for line in f.readlines() if line.strip() != ''] graph = overlapgraph.create(kmers) print(overlapgraph.graph_to_string(graph))