def test_expect_score():
colA = 'AAAAT'
colB = 'TCCCA'
score, _ = CompTools.null_score(colA, colB)
cor_score = -0.62 # by hand
eq_(score, cor_score, 'Wrong result compared to the hand-calculation')
def test_score_groups():
colA = 'AAAAT'
colB = 'TCCCA'
score, _ = CompTools.group_score(colA, colB)
cor_score = -0.8 # by hand
eq_(score, cor_score, 'Wrong result compared to the hand-calculation')
def test_group_score_seq():
groupA = [('name1', 'AA'),
('name1', 'AA'),
('name1', 'AA'),
('name1', 'AA'),
('name1', 'TT')]
groupB = [('name1', 'TT'),
('name1', 'CC'),
('name1', 'CC'),
('name1', 'CC'),
('name1', 'AA')]
df = CompTools.group_score_seq(groupA, groupB, has_names=True)
yield ok_, np.all(df['InterMu'] == -0.8), 'Group scores are incorrect!'
yield ok_, np.all(df['NullMu'] == -0.62), 'Null scores are incorrect!'
groupA = [seq for _, seq in groupA]
groupB = [seq for _, seq in groupB]
df = CompTools.group_score_seq(groupA, groupB, has_names=False)
yield ok_, np.all(df['InterMu'] == -0.8), 'Group scores are incorrect!'
yield ok_, np.all(df['NullMu'] == -0.62), 'Null scores are incorrect!'
def test_load_sub_mat():
tmp = """
H WILL-TEST
D A test matrix
R PMID: 2051488
A Dampier, W
T A matrix to test my ability to load in the data
J Will dampier's code
M rows = ACGT, cols = ACGT
0
-3. 0
-7. -1. 0
-4. 3. 2. 0
"""
ID, desc, pmid, author, text, out_dict = CompTools.load_sub_mat(tmp)
cor_ID = "WILL-TEST"
cor_desc = "A test matrix"
cor_pmid = "PMID: 2051488"
cor_author = "Dampier, W"
cor_text = "A matrix to test my ability to load in the data"
cor_dict = {('A', 'A'): 0,
('A', 'C'): -3,
('A', 'G'): -7,
('A', 'T'): -4,
('C', 'A'): -3,
('C', 'C'): 0,
('C', 'G'): -1,
('C', 'T'): 3,
('G', 'A'): -7,
('G', 'C'): -1,
('G', 'G'): 0,
('G', 'T'): 2,
('T', 'A'): -4,
('T', 'C'): 3,
('T', 'G'): 2,
('T', 'T'): 0}
yield eq_, cor_ID, ID
yield eq_, cor_desc, desc
yield eq_, cor_pmid, pmid
yield eq_, cor_author, author
yield eq_, cor_text, text
for key, val in cor_dict.items():
yield eq_, val, out_dict.get(key, None), 'Incorrect value at (%s, %s)' % key
def test_load_dist_mats():
direc = os.path.dirname(os.path.abspath(__file__))
path = os.path.join(direc, 'HIVDBFiles', 'aa_sub_mat.txt')
wanted_IDs = []
with open(path) as handle:
for line in handle:
if line.startswith('H '):
wanted_IDs.append(line.strip().split(None, 1)[-1])
test_iter = CompTools.load_dist_mats()
for out_tup, wanted_id in zip(test_iter, wanted_IDs):
ID, desc, pmid, author, text, out_dict = out_tup
yield eq_, ID, wanted_id, 'Incorrect ID found'
#eq_(ID, wanted_id, 'Incorrect ID found')
missing = []
for tup in product('ARNDCQEGHILKMFPSTWYV', 'ARNDCQEGHILKMFPSTWYV'):
if tup not in out_dict:
missing.append(tup)
#ok_(len(missing) == 0, '%s was missing %i items!' % (ID, len(missing)))
yield ok_, len(missing) == 0, '%s was missing %i items!' % (ID, len(missing))