How to use the comparem.classify.Classify function in comparem

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github dparks1134 / CompareM / comparem / main.py View on Github external
def classify(self, options):
        """Classify genomes based on AAI values."""
        check_file_exists(options.sorted_hit_table)
        make_sure_path_exists(options.output_dir)
        
        classify = Classify(options.cpus)
        results_file = classify.run(options.query_gene_file,
                                        options.target_gene_file,
                                        options.sorted_hit_table,
                                        options.evalue,
                                        options.per_identity,
                                        options.per_aln_len,
                                        options.num_top_targets,
                                        options.taxonomy_file,
                                        options.keep_rbhs,
                                        options.output_dir)
        
        self.logger.info('Classification results written to: %s' % results_file)