def align(self, options): """Create MSA from marker genes. Parameters ---------- options : argparse.Namespace The CLI arguments input by the user. """ check_dir_exists(options.identify_dir) make_sure_path_exists(options.out_dir) markers = Markers(options.cpus, options.debug) markers.align(options.identify_dir, options.skip_gtdb_refs, options.taxa_filter, options.min_perc_aa, options.custom_msa_filters, options.skip_trimming, options.rnd_seed, options.cols_per_gene, options.min_consensus, options.max_consensus, options.min_perc_taxa, options.out_dir, options.prefix, options.outgroup_taxon if hasattr(options, 'outgroup_taxon') else None, self.genomes_to_process) self.logger.info('Done.')
def identify(self, options): """Identify marker genes in genomes. Parameters ---------- options : argparse.Namespace The CLI arguments input by the user. """ if options.genome_dir: check_dir_exists(options.genome_dir) if options.batchfile: check_file_exists(options.batchfile) make_sure_path_exists(options.out_dir) genomes, tln_tables = self._genomes_to_process(options.genome_dir, options.batchfile, options.extension) self.genomes_to_process = genomes markers = Markers(options.cpus) markers.identify(genomes, tln_tables, options.out_dir, options.prefix, options.force, options.write_single_copy_genes) self.logger.info('Done.')