def test_r2prof_default(self):
"""Tests that the default rate2site instantiation produces the right profile"""
test = am.Rate4Site(self.filepath + os.sep + 'multiFasta.fasta')
output = test.rate2profile(self.filepath + os.sep + 'multiFasta.res')
self.assertTrue('Amino Acid' in output)
self.assertTrue('Conservation Score' in output)
self.assertEqual(2, len(output))
self.assertTrue(isinstance(output, biskit.ProfileCollection))
def test_r4s_close(self):
"""Tests to see that close deletes the correct files"""
r4sobject = am.Rate4Site(self.filepath + os.sep + 'multiFasta.aln')
r4sobject.run()
self.assertTrue(os.path.isfile(os.getcwd() + os.sep +
'multiFasta.res'))
r4sobject.close()
self.assertFalse(
os.path.isfile(os.getcwd() + os.sep + 'multiFasta.res'))
self.assertFalse(os.path.isdir(os.getcwd() + os.sep + 'multiFasta'))
def test_r2prof(self):
"""tests that rate2profile correctly creates profile collections with the correct output"""
test = am.Rate4Site(self.filepath + os.sep + 'multiFasta.fasta',
qqint=True,
std=True,
gapped=True)
output = test.rate2profile(self.filepath + os.sep + 'multiFasta.res')
self.assertEqual(5, len(output))
self.assertTrue('Amino Acid' in output)
self.assertTrue('Conservation Score' in output)
self.assertTrue('Standard Deviation' in output)
self.assertTrue('QQ interval' in output)
self.assertTrue('Gapped' in output)
self.assertTrue(isinstance(output, biskit.ProfileCollection))
def test_r2mat_g(self):
"""Tests that r2mat outputs the correct defaults for the dictionary"""
test = am.Rate4Site(self.filepath + os.sep + 'multiFasta.fasta')
output = test.rate2dict(self.filepath + os.sep + 'multiFasta.res')
dictionary = {
0: ('A', 0.6979),
1: ('A', 0.6979),
2: ('C', 0.7026),
3: ('C', 0.7026),
4: ('G', 0.1769),
5: ('G', 0.1769),
6: ('T', -1.577),
7: ('T', -1.577)
}
self.assertDictEqual(dictionary, output)
def test_r2mat_multi(self):
"""Tests that the correct dictionary is output when some parameters are set"""
test = am.Rate4Site(self.filepath + os.sep + 'multiFasta.fasta',
score=True,
qqint=True,
gapped=True)
output = test.rate2dict(self.filepath + os.sep + 'multiFasta.res')
dictionary = {
0: ('A', 0.6979, (-1.946, 2.735), '3/3'),
1: ('A', 0.6979, (-1.946, 2.735), '3/3'),
2: ('C', 0.7026, (-1.946, 2.735), '3/3'),
3: ('C', 0.7026, (-1.946, 2.735), '3/3'),
4: ('G', 0.1769, (-2.332, 1.853), '3/3'),
5: ('G', 0.1769, (-2.332, 1.853), '3/3'),
6: ('T', -1.577, (-3.889, -0.7852), '3/3'),
7: ('T', -1.577, (-3.889, -0.7852), '3/3')
}
self.assertDictEqual(output, dictionary)
def test_r2mat_score(self):
"""Tests that correct dictionary is output when other parameters are set"""
test = am.Rate4Site(self.filepath + os.sep + 'multiFasta.fasta',
score=False,
qqint=True,
gapped=True,
std=True)
output = test.rate2dict(self.filepath + os.sep + 'multiFasta.res')
dictionary = {
0: ('A', (-1.946, 2.735), 2.836, '3/3'),
1: ('A', (-1.946, 2.735), 2.836, '3/3'),
2: ('C', (-1.946, 2.735), 2.836, '3/3'),
3: ('C', (-1.946, 2.735), 2.836, '3/3'),
4: ('G', (-2.332, 1.853), 2.725, '3/3'),
5: ('G', (-2.332, 1.853), 2.725, '3/3'),
6: ('T', (-3.889, -0.7852), 2.309, '3/3'),
7: ('T', (-3.889, -0.7852), 2.309, '3/3')
}
self.assertDictEqual(output, dictionary)
def call_rate4site(self, msa):
"""
Calls Rate4Site to calculate various statistics of the amino acids in the input sequence
Args:
msa(str): The filepath to the file containing the msa
Returns:
The alpha parameter of the data
"""
conservation_score = aminoCons.Rate4Site(msa,
profile=self.profile,
cache=self.cache,
identity=self.identity,
score=self.score,
qqint=self.qqint,
gapped=self.gapped,
std=self.std)
self.scores = conservation_score.run()
self.alpha = conservation_score.alpha
conservation_score.close()
return self.alpha
