def align(self, options): """Create MSA from marker genes.""" check_dir_exists(options.identify_dir) make_sure_path_exists(options.out_dir) if not hasattr(options, 'outgroup_taxon'): options.outgroup_taxon = None markers = Markers(options.cpus) markers.align(options.identify_dir, options.taxa_filter, options.min_perc_aa, options.custom_msa_filters, options.consensus, options.min_perc_taxa, options.out_dir, options.prefix, options.outgroup_taxon) self.logger.info('Done.')