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 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 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.')
def setUp(self):
self.classify = Classify()
self.out_dir = tempfile.mkdtemp(prefix='gtdbtk_tmp_')
self.prefix = 'gtdbtk'
self.pplacer_dir_reference = 'tests/data/pplacer_dir_reference'
self.aln_dir_ref = 'tests/data/align_dir_reference/align'
self.user_msa_file = os.path.join(self.aln_dir_ref, 'gtdbtk.ar122.user_msa.fasta')
self.taxonomy_file = Config.TAXONOMY_FILE
self.gtdb_taxonomy = Taxonomy().read(self.taxonomy_file)
def setUp(self):
self.classify = Classify()
self.generic_out_path = 'tests/data/results'
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
self.out_dir = os.path.join(self.generic_out_path, tmp_folder)
if not os.path.exists(self.generic_out_path):
os.makedirs(self.generic_out_path)
self.prefix = 'gtdbtk'
self.pplacer_dir_reference = 'tests/data/pplacer_dir_reference'
self.user_msa_file = os.path.join(
self.pplacer_dir_reference, 'gtdbtk.ar122.user_msa.fasta')
self.taxonomy_file = Config.TAXONOMY_FILE
self.gtdb_taxonomy = Taxonomy().read(self.taxonomy_file)