def getPValueLoose(self, module, alphabet_len=None):
"""Returns the Pvalue of a module.
- pass alphabet_len if alphabet other than module.MolType was used
to find modules (i.e. using a protein reduced alphabet)
"""
# Length of the module
module_len = len(module.Template)
# if moltype length has not been passed, get it from module.MolType
#
if not alphabet_len:
alphabet_len = len(module.MolType.Alphabet)
# Total length of the alignment
aln_len = sum(map(len, self.Alignment.values()))
# Number of sequences in the alignment
num_seqs = len(self.Alignment)
# get module_p
module_p = 1
for char in module.Template:
module_p *= self._degen_p(char, module.MolType)
# Mean for passing to poisson_high using loose correction
loose_mean = (aln_len + num_seqs * (1 - module_len)) * (module_p)
# Loose P value from poisson_high
loose_p_value = poisson_high(len(module) - 1, loose_mean)
# Correct P value for multiple comparisons
loose_p_corrected = multiple_comparisons(loose_p_value, alphabet_len ** module_len)
return loose_p_corrected
def getPValueLoose(self, module, alphabet_len=None):
"""Returns the Pvalue of a module.
- pass alphabet_len if alphabet other than module.MolType was used
to find modules (i.e. using a protein reduced alphabet)
"""
#Length of the module
module_len = len(module.Template)
#if moltype length has not been passed, get it from module.MolType
#
if not alphabet_len:
alphabet_len = len(module.MolType.Alphabet)
#Total length of the alignment
aln_len = sum(map(len, self.Alignment.values()))
#Number of sequences in the alignment
num_seqs = len(self.Alignment)
#get module_p
module_p = 1
for char in module.Template:
module_p *= self._degen_p(char, module.MolType)
#Mean for passing to poisson_high using loose correction
loose_mean = \
(aln_len + num_seqs*(1-module_len))*(module_p)
#Loose P value from poisson_high
loose_p_value = poisson_high(len(module) - 1, loose_mean)
#Correct P value for multiple comparisons
loose_p_corrected = \
multiple_comparisons(loose_p_value,alphabet_len**module_len)
return loose_p_corrected
def test_poisson_high(self):
"""Upper tail of poisson should match R for integer successes"""
#WARNING: Results only guaranteed for integer successes: floating
#point _should_ yield reasonable values, but R rounds to int.
expected = {
(0, 0): 0,
(0, 0.75): 0.5276334,
(0, 1): 0.6321206,
(0, 5): 0.993262,
(0, 113.7): 1,
(2, 0): 0,
(2, 3): 0.5768099,
(2, 17.8): 0.9999967,
(17, 29.6): 0.9912467,
(180, 0): 0,
(180, 137.4):0.0002159856,
(180, 318):1,
(180, 1024):1,
}
for (key, value) in expected.items():
self.assertFloatEqual(poisson_high(*key), value)