Beispiel #1
0
 def score(self,site,both_strands=False):
     ef = self.directional_score(site)
     if both_strands:
         eb = self.directional_score(wc(site))
         return log(exp(beta*ef) + exp(beta*eb))/(beta)
     else:
         return ef
Beispiel #2
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 def binding_energy(self,site,double_stranded=False):
     """Compute binding energy of site.  See calcBindingEnergy,Organism.cpp"""
     w = len(site)
     E_f = self.activation(site) * w * (-2/beta) - 0.05
     E_b = double_stranded and (self.activation(wc(site)) * w * (-2/beta) - 0.05)
     E_t = ((1 / -beta) * log(exp(-beta * E_f) + exp(-beta * E_b))
            if double_stranded
            else E_f)
     return E_t
Beispiel #3
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 def __init__(self,seq_line):
     fields = seq_line.split(",")
     numeric_fields = map(float,fields[1:])
     self.site = fields[0]
     (self.position,
      self.strand,
      self.ep,
      self.act,
      self.tProb,
      self.gc,
      self.tConc) = numeric_fields[:7]
     self.position_energies = map(float,fields[6:])
     self.complements = sum(map(lambda(x,y):x==y,zip(self.site,wc(self.site))))
Beispiel #4
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 def adjust(site):
     if self.recognizer.score(site) < self.recognizer.score(wc(site)):
         return site
     else:
         return wc(site)
Beispiel #5
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 def matched_base_pairs(self):
     return sum(map(lambda(x,y):x==y,
                    zip(self.site,wc(self.site))))