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])
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 ])
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])