def get_alpha(r4s):
"""
Get the alpha parameter of the conservation scores, as defined by rate4site
Args:
r4s (file): The absolute file path to the alignment file
Returns:
The alpha parameter of the conservation score.
"""
try:
if os.path.isfile(r4s):
with open(r4s, 'r') as f:
contents = f.read()
splitted = contents.split(os.linesep)
for s in splitted:
if re.search('alpha parameter', s):
parameter = constool.get_num(s)
return parameter[0]
raise Rate4SiteError('File format is not supported')
else:
raise FileNotFoundError
except IndexError:
raise Rate4SiteError('File format is not supported')
finally:
warnings.warn("This method is especially susceptible to changes in the format of \
the output file", Warning)
def test_get_num_negative(self):
"""Tests that get_num can retrieve negative and positive numbers from within a string"""
digit = constool.get_num(
"Hello, how are all 1234.56 and -42 of you today")
self.assertEqual(digit, [1234.56, -42])
def test_get_num_none(self):
"""Tests that a string containing no digits returns no digits"""
digit = constool.get_num("Oh, there are none of you today")
self.assertEqual(digit, [])
def test_get_num_multi(self):
"""Tests that get_num can retrieve multiple floats and integers from a string """
digit = constool.get_num(
"Hello, how are all 1234.56 and 42 of you today")
self.assertEqual(digit, [1234.56, 42])
def test_get_num_good(self):
"""Tests that get num can retrieve a single float from a string"""
digit = constool.get_num("Hello, how are all 1234.56 of you today")
self.assertEqual(digit[0], 1234.56)