Python hamming_distance Examples

Example #1

File: virus_clean.py Project: blab/stability

	def distance_from_outgroup(self, start=0, stop=0):
		from seq_util import hamming_distance
		outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
		if stop==0:
			stop=len(outgroup_seq)
		outgroup_seq = outgroup_seq[start:stop]
		return np.array([hamming_distance(x.seq[start:stop], outgroup_seq) 
			   for x in self.viruses if x.strain])

Example #2

 def distance_from_outgroup(self, start=0, stop=0):
     from seq_util import hamming_distance
     outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
     if stop == 0:
         stop = len(outgroup_seq)
     outgroup_seq = outgroup_seq[start:stop]
     return np.array([
         hamming_distance(x.seq[start:stop], outgroup_seq)
         for x in self.viruses if x.strain
     ])

Example #3

File: virus_clean.py Project: 5l1v3r1/treetool

	def distance_from_outgroup(self):
		from seq_util import hamming_distance
		outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
		return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain])