sequences_process.py 文件源码

def export_diversity(self, fname = 'entropy.json', indent=None):
        '''
        write the alignment entropy of each alignment (nucleotide and translations) to file
        '''
        if not hasattr(self, "entropy"):
            self.diversity_statistics()
        entropy_json = {}
        for feat in self.entropy:
            S = [max(0,round(x,4)) for x in self.entropy[feat]]
            n = len(S)
            if feat=='nuc':
                entropy_json[feat] = {'pos':range(0,n), 'codon':[x//3 for x in range(0,n)], 'val':S}
            else:
                entropy_json[feat] = {'pos':[x for x in self.proteins[feat]][::3],
                                      'codon':[(x-self.proteins[feat].start)//3 for x in self.proteins[feat]][::3], 'val':S}
        write_json(entropy_json, fname, indent=indent)