dbotu.py 文件源码

def _process_record(self, record_id):
        '''
        Process the next sequence: run the genetic, abundance, and distribution checks, either
        merging the sequence into an existing OTU or creating a new OTU.
        '''
        assert record_id in self.seq_table.index
        record = self.records[record_id]

        candidate = OTU(record.id, str(record.seq), self.seq_table.loc[record.id])

        if self.log is not None:
            print('seq', candidate.name, sep='\t', file=self.log)

        merged = False
        for otu in self.ga_matches(candidate):
            test_pval = candidate.distribution_pval(otu)

            if self.log is not None:
                print(candidate.name, 'distribution_check', otu.name, test_pval, sep='\t', file=self.log)

            if test_pval > self.threshold_pval:
                otu.absorb(candidate)
                self.membership[otu.name].append(candidate.name)
                merged = True
                break

        if not merged:
            # form own otu
            self.otus.append(candidate)
            self.membership[candidate.name] = [candidate.name]