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.')
