def classify(self, options):
"""Determine taxonomic classification of genomes.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
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, options.pplacer_cpus, options.min_af)
classify.run(genomes,
options.align_dir,
options.out_dir,
options.prefix,
options.scratch_dir,
options.recalculate_red,
options.debug,
options.split_tree)
self.logger.info('Done.')
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 classify(self, options):
"""Determine taxonomic classification of genomes.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
# See ticket #255... perhaps an upstream version/OS issue?
if not hasattr(options, 'pplacer_cpus'):
options.pplacer_cpus = None
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, options.pplacer_cpus)
classify.run(genomes, options.align_dir, options.out_dir,
options.prefix, options.scratch_dir,
options.recalculate_red, options.debug,
options.split_tree)
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.')
def classify(self, options):
"""Determine taxonomic classification of genomes.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
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, options.pplacer_cpus, options.min_af)
classify.run(genomes=genomes,
align_dir=options.align_dir,
out_dir=options.out_dir,
prefix=options.prefix,
scratch_dir=options.scratch_dir,
debugopt=options.debug,
fulltreeopt=options.full_tree,
recalculate_red=False)
self.logger.info(
'Note that Tk classification mode is insufficient for publication of new taxonomic '
'designations. New designations should be based on one or more de novo trees, an '
'example of which can be produced by Tk in de novo mode.')
self.logger.info('Done.')
