sequences_process.py 文件源码

def make_gaps_ambiguous(self):
        '''
        replace all gaps by 'N' in all sequences in the alignment. TreeTime will treat them
        as fully ambiguous and replace then with the most likely state
        '''
        for seq in self.aln:
            seq_array = np.array(seq)
            gaps = seq_array=='-'
            seq_array[gaps]='N'
            seq.seq = Seq("".join(seq_array))