def _test(self, data_file_path):
with open(data_file_path, 'r') as datafile:
lines = [line.strip() for line in datafile.readlines()]
dna = lines[1]
peptide = lines[2]
expected = lines[4:]
actual = find_peptide_encoding(dna, peptide)
self.assertTrue(AreStringListsEqual(expected, actual))
def _test(self, data_file_path):
with open(data_file_path, 'r') as datafile:
lines = [line.strip() for line in datafile.readlines()]
n = int(lines[1])
spectrum = [int(mass) for mass in lines[2].split(' ')]
expected = lines[4].split('-')
actual = [str(mass) for mass in leaderboard_cyclopeptide(spectrum, n)]
self.assertTrue(AreStringListsEqual(expected, actual))
def _test(self, datafile_name):
with open(datafile_name, 'r') as datafile:
lines = [line.strip() for line in datafile.readlines()]
index_of_output_start = lines.index("Output:")
kmers = lines[1:index_of_output_start]
expected = lines[index_of_output_start + 1:]
result = generate_contigs(kmers)
self.assertTrue(AreStringListsEqual(expected, result))
def _test(self, datafile_name):
with open(datafile_name, 'r') as datafile:
lines = datafile.readlines()
k = int(lines[1].strip())
text = lines[2].strip()
expected_outputs = [line.strip() for line in lines[4:]]
outputs = construct_de_Bruijn_graph(k, text)
self.assertTrue(AreStringListsEqual(expected_outputs, outputs))
def _test(self, data_file_path):
with open(data_file_path, 'r') as datafile:
lines = [line.strip() for line in datafile.readlines()]
m = int(lines[1])
n = int(lines[2])
spectrum = [int(mass) for mass in lines[3].split(' ')]
expected = lines[5].split('-')
actual = [str(mass) for mass in convolution_cyclopeptide_sequencing(m, n, spectrum)]
self.assertTrue(AreStringListsEqual(expected, actual))
def _test(self, data_file_path):
with open(data_file_path, 'r') as datafile:
lines = [line.strip() for line in datafile.readlines()]
leaderboard = lines[1].split(' ')
spectrum = [int(mass) for mass in lines[2].split(' ')]
n = int(lines[3])
expected = lines[5].split(' ')
actual = trim(leaderboard, spectrum, n)
self.assertTrue(AreStringListsEqual(expected, actual))
def _test(self, datafile_name):
with open(datafile_name, 'r') as datafile:
lines = datafile.readlines()
k = int(lines[1].strip())
text = lines[2].strip()
expected_compositions = [line.strip() for line in lines[4:]]
compositions = string_composition(k, text)
self.assertTrue(
AreStringListsEqual(expected_compositions, compositions))
def _test(self, datafile_name):
with open(datafile_name, 'r') as datafile:
datafile.readline() # "Input"
args = datafile.readline().strip().split(" ")
k = int(args[0])
t = int(args[1])
dnas = []
for i in range(t):
dnas.append(datafile.readline().strip())
datafile.readline() # "Output"
expected_motifs = []
for i in range(t):
expected_motifs.append(datafile.readline().strip())
motifs = greedy_motif_search_laplace(dnas, k)
self.assertTrue(AreStringListsEqual(expected_motifs, motifs))
def _test(self, datafile_name):
with open(datafile_name, 'r') as datafile:
kmers = []
expected_outputs = []
current_data_set = None
while True:
line = datafile.readline().strip()
if not line:
break
if line.__contains__("Input"):
current_data_set = kmers
elif line.__contains__("Output"):
current_data_set = expected_outputs
else:
current_data_set.append(line)
outputs = construct_de_Bruijn_graph_from_kmers(kmers)
self.assertTrue(AreStringListsEqual(expected_outputs, outputs))
def _test(self, datafile_name):
with open(datafile_name, 'r') as datafile:
datafile.readline() # "Input"
args = datafile.readline().strip().split(" ")
k = int(args[0])
t = int(args[1])
dna_list = []
for i in range(t):
dna_list.append(datafile.readline().strip())
datafile.readline() # "Output"
expected_motifs = []
for i in range(t):
expected_motifs.append(datafile.readline().strip())
motifs = randomized_motif_search(dna_list, k, t)
passed = AreStringListsEqual(expected_motifs, motifs)
if not passed:
print("Expected: " + ' '.join(expected_motifs))
print("Actual: " + ' '.join(motifs))
self.assertTrue(passed)