Esempio n. 1
0
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)
Esempio n. 2
0
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))