def classify(self, options): """Determine taxonomic classification of genomes.""" check_dir_exists(options.align_dir) make_sure_path_exists(options.out_dir) if options.scratch_dir: make_sure_path_exists(options.scratch_dir) genomes = self._genomes_to_process(options.genome_dir, options.batchfile, options.extension) classify = Classify(options.cpus) classify.run(genomes, options.align_dir, options.out_dir, options.prefix, options.scratch_dir, options.debug) self.logger.info('Done.')
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.skip_gtdb_refs, options.taxa_filter, options.min_perc_aa, options.custom_msa_filters, 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) self.logger.info('Done.')
def identify(self, options): """Identify marker genes in genomes.""" 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 = self._genomes_to_process(options.genome_dir, options.batchfile, options.extension) markers = Markers(options.cpus) markers.identify(genomes, options.out_dir, options.prefix) self.logger.info('Done.')