def std(self, background=None):
"""Standard deviation of the score of a motif."""
if background is None:
background = dict.fromkeys(self._letters, 1.0)
else:
background = dict(background)
total = sum(background.values())
for letter in self._letters:
background[letter] /= total
variance = 0.0
for i in range(self.length):
sx = 0.0
sxx = 0.0
for letter in self._letters:
logodds = self[letter, i]
if _isnan(logodds):
continue
if _isinf(logodds) and logodds < 0:
continue
b = background[letter]
p = b * math.pow(2, logodds)
sx += p * logodds
sxx += p * logodds * logodds
sxx -= sx * sx
variance += sxx
variance = max(variance, 0) # to avoid roundoff problems
return math.sqrt(variance)
def std(self, background=None):
"""Standard deviation of the score of a motif."""
if background is None:
background = dict.fromkeys(self._letters, 1.0)
else:
background = dict(background)
total = sum(background.values())
for letter in self._letters:
background[letter] /= total
variance = 0.0
for i in range(self.length):
sx = 0.0
sxx = 0.0
for letter in self._letters:
logodds = self[letter, i]
if _isnan(logodds):
continue
if _isinf(logodds) and logodds < 0:
continue
b = background[letter]
p = b * math.pow(2, logodds)
sx += p*logodds
sxx += p*logodds*logodds
sxx -= sx*sx
variance += sxx
variance = max(variance, 0) # to avoid roundoff problems
return math.sqrt(variance)
def mean(self, background=None):
"""Expected value of the score of a motif."""
if background is None:
background = dict.fromkeys(self._letters, 1.0)
else:
background = dict(background)
total = sum(background.values())
for letter in self._letters:
background[letter] /= total
sx = 0.0
for i in range(self.length):
for letter in self._letters:
logodds = self[letter, i]
if _isnan(logodds):
continue
if _isinf(logodds) and logodds < 0:
continue
b = background[letter]
p = b * math.pow(2, logodds)
sx += p * logodds
return sx
def mean(self, background=None):
"""Expected value of the score of a motif."""
if background is None:
background = dict.fromkeys(self._letters, 1.0)
else:
background = dict(background)
total = sum(background.values())
for letter in self._letters:
background[letter] /= total
sx = 0.0
for i in range(self.length):
for letter in self._letters:
logodds = self[letter, i]
if _isnan(logodds):
continue
if _isinf(logodds) and logodds < 0:
continue
b = background[letter]
p = b * math.pow(2, logodds)
sx += p * logodds
return sx