예제 #1
0
파일: matrix.py 프로젝트: cbirdlab/sap
 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)
예제 #2
0
 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)
예제 #3
0
파일: matrix.py 프로젝트: cbirdlab/sap
 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
예제 #4
0
 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