dbotu.py 文件源码

def ga_matches(self, candidate):
        '''
        OTUs that meet the genetic and abundance criteria

        candidate: OTU
          sequence to evaluate
        '''

        # find abundance matches
        min_abundance = self.min_fold * candidate.abundance
        abundance_matches = [otu for otu in self.otus if otu.abundance > min_abundance]

        if self.log is not None:
            print(candidate.name, 'abundance_check', *[otu.name for otu in abundance_matches], sep='\t', file=self.log)

        if len(abundance_matches) == 0:
            return []
        else:
            # find genetic matches (in order of decreasing genetic distance)
            matches_distances = [(otu.distance_to(candidate), otu) for otu in abundance_matches]
            matches_distances.sort(key=lambda x: (x[0], -x[1].abundance, x[1].name))
            matches = [otu for dist, otu in matches_distances if dist < self.max_dist]

            if self.log is not None:
                print(candidate.name, 'genetic_check', *[otu.name for otu in matches], sep='\t', file=self.log)

            return matches