def run_test(self, k, seq_name, expected_name):
with open(util.find_file(seq_name, __file__), "r") as fp:
fp.readline() # skip count
seq = fp.readline().strip()
expected = seqio.read_list(expected_name, __file__)
actual = main.generate_kmers(seq, k)
self.assertItemsEqual(actual, expected)
def test_sample2(self):
with open(util.find_file("sample2.txt", __file__), "r") as fp:
dna = fp.readline().strip()
protein = fp.readline().strip()
expected = seqio.read_list("expected2.txt", __file__)
actual = main.find_encodings(dna, protein)
self.assertItemsEqual(actual, expected)
def main(fname):
start = time.time()
seqs = seqio.read_list(sys.argv[1])
result = build_overlap_graph(seqs)
for p in result:
print (p[0], "->", p[1])
end = time.time()
eprint(round((end - start), 5))
def run_test(self, sample_name, expected_name):
seqs = seqio.read_list(sample_name, __file__)
expected = []
with open(util.find_file(expected_name, __file__), "r") as fp:
for line in fp:
bits = line.strip().split()
expected.append((bits[0], bits[2]))
actual = main.build_overlap_graph(seqs)
self.assertItemsEqual(actual, expected)
def run_test(self, sample_name, expected_name):
seqs, _ = fasta.read(util.find_file(sample_name, __file__))
expected = seqio.read_list(util.find_file(expected_name, __file__))
actual = main.find_corrections(seqs)
self.assertItemsEqual(actual, expected)
def main(fname):
seqs = seqio.read_list(fname, __file__)
chromosome = assemble_circular_chromosome(seqs)
print chromosome
def test_sample1(self):
seqs = seqio.read_list("sample1.txt", __file__)
expected = "GATTACA"
self.run_test(seqs, expected)
def test_sample2(self):
seqs = seqio.read_list("sample2.txt", __file__)
expected = seqio.read_one("expected2.txt", __file__)
self.run_test(seqs, expected)
def run_test(self, sample_name, expected_name):
seqs = seqio.read_list(sample_name, __file__)
expected = seqio.read_one(expected_name, __file__)
actual = main.reconstruct_string(seqs)
self.assertEquals(actual, expected)
def main(fname):
seqs = seqio.read_list(fname)
graph = make_graph(seqs)
for line in debruijn.format_adjacency(graph):
print line