def test_create(): k = 4 text = 'AAGATTCTCTAAGA' expected = {'AAG': ['AGA', 'AGA'], 'TCT': ['CTC', 'CTA'], 'GAT': ['ATT'], 'AGA': ['GAT'], 'ATT': ['TTC'], 'CTA': ['TAA'], 'CTC': ['TCT'], 'TTC': ['TCT'], 'TAA': ['AAG']} actual = debruijn.create(text, k) assert (expected == actual)
import debruijn, sys mode = sys.argv[1] filename = sys.argv[2] with open(filename, 'r') as f: if mode == 'patterns': kmers = [line.strip() for line in f.readlines() if line.strip() != ''] graph = debruijn.create_from_patterns(kmers) else: k = int(f.readline()) text = f.readline() graph = debruijn.create(text, k) print(debruijn.to_string(graph))