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,
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)
class TestClassify(unittest.TestCase):
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.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 test_standardise_taxonomy(self):
taxstring = 'p__phylum1;c_class1'
marker_set = 'bac120'
new_taxstring = self.classify.standardise_taxonomy(
taxstring, marker_set)
self.assertEqual(new_taxstring,
'd__Bacteria;p__phylum1;c_class1;o__;f__;g__;s__')
# Test that the correct domain is returned.
self.assertEqual(
self.classify.standardise_taxonomy('p__P;c__C;o__O;f__F;g__G;s__S',
'bac120'),
'd__Bacteria;p__P;c__C;o__O;f__F;g__G;s__S')
self.assertEqual(
self.classify.standardise_taxonomy('p__P;c__C;o__O;f__F;g__G;s__S',
'ar122'),
'd__Archaea;p__P;c__C;o__O;f__F;g__G;s__S')
# Remove ranks and check
rank_order = {'p': 0, 'c': 1, 'o': 2, 'f': 3, 'g': 4, 's': 5}
rank_lst = ['p__P', 'c__C', 'o__O', 'f__F', 'g__G', 's__S']
ranks = {'p': 'P', 'c': 'C', 'o': 'O', 'f': 'F', 'g': 'G', 's': 'S'}
dom_info = {'d__Bacteria': 'bac120', 'd__Archaea': 'ar122'}
for k in range(1, len(ranks) - 1):
for cur_domain in ('d__Bacteria', 'd__Archaea'):
ranks_selected = rank_lst[0:-k]
expected = list()
test_lst = list()
for cur_rank, _ in sorted(rank_order.items(),
key=lambda x: [1]):
if cur_rank in ranks_selected:
test_lst.append(f'{cur_rank}__{ranks[cur_rank]}')
expected.append(f'{cur_rank}__{ranks[cur_rank]}')
else:
expected.append(f'{cur_rank}__')
expected_str = f'{cur_domain};{";".join(expected)}'
test_str = ";".join(test_lst)
cur_dom = dom_info[cur_domain]
test_value = self.classify.standardise_taxonomy(
test_str, cur_dom)
self.assertEqual(expected_str, test_value)
def test_write_red_dict(self):
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
marker_dict = self.classify._write_red_dict(self.out_dir, self.prefix,
'bac120')
self.assertTrue(len(marker_dict) == 6)
self.assertTrue('d__' in marker_dict)
self.assertTrue(marker_dict.get('d__') == 0)
self.assertTrue('p__' in marker_dict)
self.assertTrue('c__' in marker_dict)
self.assertTrue('o__' in marker_dict)
self.assertTrue('f__' in marker_dict)
self.assertTrue('g__' in marker_dict)
def test_get_pplacer_taxonomy(self):
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
tree = dendropy.Tree.get_from_path(os.path.join(
os.getcwd(), self.pplacer_dir_reference,
'gtdbtk.ar122.classify.tree'),
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
self.classify._get_pplacer_taxonomy(self.out_dir, self.prefix, 'ar122',
self.user_msa_file, tree)
results = {}
with open(
os.path.join(
self.out_dir,
PATH_AR122_PPLACER_CLASS.format(prefix=self.prefix)),
'r') as f:
for line in f:
infos = line.strip().split('\t')
results[infos[0]] = infos[1]
self.assertTrue(len(results) == 3)
self.assertTrue('genome_1' in results)
self.assertTrue('genome_2' in results)
self.assertTrue('genome_3' in results)
self.assertEqual(
results.get('genome_1'),
'd__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__'
)
def test_place_genomes(self):
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
tree_file = self.classify.place_genomes(self.user_msa_file, 'ar122',
self.out_dir, self.prefix)
with open(tree_file, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(last_line.startswith('('))
self.assertTrue(last_line.endswith('d__Archaea;'))
def test_formatnote(self):
first3genomes = list(self.gtdb_taxonomy.keys())[:3]
sorted_dict = ((first3genomes[0], {
'ani': 98.5,
'af': 1.0
}), (first3genomes[1], {
'ani': 92.6,
'af': 1.0
}), (first3genomes[2], {
'ani': 90.3,
'af': 1.3
}))
labels = [first3genomes[0]]
note_list = self.classify._formatnote(sorted_dict, labels)
self.assertTrue(first3genomes[1] in note_list[0])
self.assertTrue(first3genomes[2] in note_list[1])
self.assertTrue(note_list[0].endswith(', 92.6, 1.0'))
self.assertTrue(note_list[1].endswith(', 90.3, 1.3'))
def test_calculate_red_distances(self):
tree = os.path.join(self.pplacer_dir_reference,
'gtdbtk.ar122.classify.tree')
result_tree = self.classify._calculate_red_distances(
tree, self.out_dir)
egs2 = [
eg.length for eg in result_tree.postorder_edge_iter()
if eg.length is not None
]
self.assertTrue(sum(egs2) / len(egs2) < 0.1)
def tearDown(self):
shutil.rmtree(self.generic_out_path)
class TestClassify(unittest.TestCase):
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)
def test_standardise_taxonomy(self):
taxstring = 'p__phylum1;c_class1'
marker_set = 'bac120'
new_taxstring = self.classify.standardise_taxonomy(
taxstring, marker_set)
self.assertEqual(
new_taxstring, 'd__Bacteria;p__phylum1;c_class1;o__;f__;g__;s__')
def test_write_red_dict(self):
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
marker_dict = self.classify._write_red_dict(
self.out_dir, self.prefix, 'bac120')
self.assertTrue(len(marker_dict) == 6)
self.assertTrue('d__' in marker_dict)
self.assertTrue(marker_dict.get('d__') == 0)
self.assertTrue('p__' in marker_dict)
self.assertTrue('c__' in marker_dict)
self.assertTrue('o__' in marker_dict)
self.assertTrue('f__' in marker_dict)
self.assertTrue('g__' in marker_dict)
def test_get_pplacer_taxonomy(self):
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
tree = dendropy.Tree.get_from_path(os.path.join(os.getcwd(), self.pplacer_dir_reference,
'gtdbtk.ar122.classify.tree'),
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
self.classify._get_pplacer_taxonomy(
self.out_dir, self.prefix, 'ar122', self.user_msa_file, tree)
results = {}
with open(os.path.join(self.out_dir, PATH_AR122_PPLACER_CLASS.format(prefix=self.prefix)), 'r') as f:
for line in f:
infos = line.strip().split('\t')
results[infos[0]] = infos[1]
self.assertTrue(len(results) == 3)
self.assertTrue('genome_1' in results)
self.assertTrue('genome_2' in results)
self.assertTrue('genome_3' in results)
self.assertEqual(results.get(
'genome_1'), 'd__Archaea;p__Thermoplasmatota;c__MGII;o__MGIII;f__CG-Epi1;g__UBA8886;s__')
def test_place_genomes(self):
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
tree_file = self.classify.place_genomes(
self.user_msa_file, 'ar122', self.out_dir, self.prefix)
with open(tree_file, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(last_line.startswith('('))
self.assertTrue(last_line.endswith('d__Archaea;'))
def test_formatnote(self):
first3genomes = self.gtdb_taxonomy.keys()[:3]
sorted_dict = ((first3genomes[0], {'ani': 98.5, 'af': 1.0}), (first3genomes[1], {
'ani': 92.6, 'af': 1.0}), (first3genomes[2], {'ani': 90.3, 'af': 1.3}))
labels = [first3genomes[0]]
note_list = self.classify._formatnote(sorted_dict, labels)
self.assertTrue(first3genomes[1]in note_list[0])
self.assertTrue(first3genomes[2]in note_list[1])
self.assertTrue(note_list[0].endswith(', 92.6, 1.0'))
self.assertTrue(note_list[1].endswith(', 90.3, 1.3'))
def test_calculate_red_distances(self):
tree = os.path.join(self.pplacer_dir_reference,
'gtdbtk.ar122.classify.tree')
result_tree = self.classify._calculate_red_distances(
tree, self.out_dir)
egs2 = [eg.length for eg in result_tree.postorder_edge_iter()
if eg.length is not None]
self.assertTrue(sum(egs2) / len(egs2) < 0.1)
def tearDown(self):
shutil.rmtree(self.generic_out_path)