class TestCli(unittest.TestCase):
def setUp(self):
self.identify_dir_reference = os.path.join(os.path.dirname(__file__), 'data/identify_dir_reference/')
self.align_dir_reference = 'tests/data/align_dir_reference/'
self.genome_dir = 'gtdbtk/tests/data/genomes/'
self.options = argparse.ArgumentParser()
self.options.batchfile = None
self.options.prefix = 'gtdbtk'
self.options.cpus = 1
self.options.extension = 'fna'
self.options.debug = False
self.options.force = False
self.options.genes = False
self.options.write_single_copy_genes = False
# align option
self.options.skip_gtdb_refs = False
self.options.taxa_filter = None
self.options.custom_msa_filters = False
self.options.skip_trimming = False
self.options.min_consensus = None
self.options.min_perc_taxa = None
self.options.skip_gtdb_refs = False
self.options.cols_per_gene = None
self.options.max_consensus = None
self.options.min_perc_aa = 50
self.options.rnd_seed = 42
self.options.outgroup_taxon = None
# classify options
self.options.scratch_dir = None
self.options.keep_ref_red = None
self.options.pplacer_cpus = None
self.options.min_af = None
# infer options
self.options.prot_model = 'WAG'
self.options.no_support = False
self.options.no_gamma = True
self.version = ' unittest'
self.optionparser = OptionsParser(self.version)
logger_setup(None, "gtdbtk.log", "GTDB-Tk", self.version, True)
# self.generic_out_path = 'tests/data/results'
self.generic_out_path = tempfile.mkdtemp(prefix='gtdbtk_tmp_')
def tearDown(self):
shutil.rmtree(self.generic_out_path)
def test_identify(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'identify')
self.optionparser.identify(identify_options)
ar53_marker_path = os.path.join(self.options.out_dir,
PATH_AR53_MARKER_SUMMARY.format(prefix=self.options.prefix))
self.assertTrue(os.path.isfile(
os.path.join(self.options.out_dir, PATH_BAC120_MARKER_SUMMARY.format(prefix=self.options.prefix))))
self.assertTrue(os.path.isfile(ar53_marker_path))
results = {}
with open(ar53_marker_path, 'r') as f:
f.readline()
for line in f:
infos = line.split('\t', 1)
results[infos[0]] = infos[1]
self.assertTrue(results.get('genome_1').startswith('120\t2\t0\t'))
def test_align(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
align_options = self.options
align_options.identify_dir = self.identify_dir_reference
align_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(align_options.out_dir, PATH_AR53_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_identify_align(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(
self.generic_out_path, tmp_folder, 'identify')
align_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(align_options.out_dir, PATH_AR53_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_identify_align_classify(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(
self.generic_out_path, tmp_folder, 'identify')
align_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(align_options.out_dir, PATH_AR53_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.full_tree = True
classify_options.align_dir = align_options.out_dir
classify_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'classify')
classify_options.recalculate_red = False
self.optionparser.classify(classify_options)
summary_out = os.path.join(classify_options.out_dir,
PATH_AR53_SUMMARY_OUT.format(prefix=classify_options.prefix))
self.assertTrue(summary_out)
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEqual(len(infos), 20)
self.assertTrue(infos[1].startswith('d__Archaea'))
self.assertTrue(os.path.isdir(os.path.join(classify_options.out_dir, DIR_IDENTIFY_INTERMEDIATE)))
self.assertTrue(os.path.isdir(os.path.join(classify_options.out_dir, DIR_ALIGN_INTERMEDIATE)))
self.assertTrue(os.path.isdir(os.path.join(classify_options.out_dir, DIR_CLASSIFY_INTERMEDIATE)))
self.optionparser.remove_intermediate_files(classify_options.out_dir,'classify_wf')
self.assertFalse(os.path.exists(os.path.join(classify_options.out_dir, DIR_IDENTIFY_INTERMEDIATE)))
self.assertFalse(os.path.exists(os.path.join(classify_options.out_dir, DIR_ALIGN_INTERMEDIATE)))
self.assertFalse(os.path.exists(os.path.join(classify_options.out_dir, DIR_CLASSIFY_INTERMEDIATE)))
def test_classify_wf(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
classify_wf_options = self.options
classify_wf_options.genome_dir = self.genome_dir
classify_wf_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'classify_wf')
self.optionparser.identify(classify_wf_options)
classify_wf_options.identify_dir = classify_wf_options.out_dir
classify_wf_options.align_dir = classify_wf_options.out_dir
classify_wf_options.taxa_filter = None
classify_wf_options.custom_msa_filters = False
classify_wf_options.min_consensus = None
classify_wf_options.min_perc_taxa = None
classify_wf_options.skip_gtdb_refs = False
classify_wf_options.cols_per_gene = None
classify_wf_options.max_consensus = None
classify_wf_options.recalculate_red = False
classify_wf_options.full_tree = True
self.optionparser.align(classify_wf_options)
self.optionparser.classify(classify_wf_options)
summary_out = os.path.join(classify_wf_options.out_dir,
PATH_AR53_SUMMARY_OUT.format(prefix=classify_wf_options.prefix))
self.assertTrue(os.path.isfile(summary_out))
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEqual(len(infos), 20)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_infer(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
infer_options = self.options
path_user_msa = PATH_AR53_USER_MSA.format(prefix=self.options.prefix)
infer_options.msa_file = os.path.join(self.align_dir_reference, path_user_msa)
infer_options.out_dir = os.path.join(self.generic_out_path, tmp_folder, 'infer')
infer_options.gamma = False
# if not os.path.isdir(infer_options.out_dir):
# os.makedirs(infer_options.out_dir)
self.optionparser.infer(infer_options)
with open(os.path.join(infer_options.out_dir, PATH_TREE_LOG.format(prefix=self.options.prefix)), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertEqual(last_line.strip(), 'TreeCompleted')
with open(os.path.join(infer_options.out_dir, PATH_UNROOTED_TREE.format(prefix=self.options.prefix)), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue('genome_1' in last_line)
self.assertTrue('genome_2' in last_line)
self.assertTrue('genome_3' in last_line)
def test_de_novo_wf(self):
tmp_folder = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(10))
de_novo_wf_options = self.options
de_novo_wf_options.genome_dir = self.genome_dir
de_novo_wf_options.suffix = ".ar53"
de_novo_wf_options.gamma = False
de_novo_wf_options.out_dir = os.path.join(
self.generic_out_path, tmp_folder, 'de_novo_wf')
de_novo_wf_options.identify_dir = de_novo_wf_options.out_dir
de_novo_wf_options.msa_file = os.path.join(
de_novo_wf_options.out_dir, de_novo_wf_options.prefix + de_novo_wf_options.suffix + ".user_msa.fasta")
self.optionparser.identify(de_novo_wf_options)
self.optionparser.align(de_novo_wf_options)
self.optionparser.infer(de_novo_wf_options)
def test_root(self):
"""Test that rooting is successful when called through the CLI"""
options = argparse.ArgumentParser()
options.input_tree = 'tests/data/pplacer_dir_reference/gtdbtk.ar53.classify.tree'
options.outgroup_taxon = 'p__Altiarchaeota'
options.output_tree = os.path.join(self.generic_out_path, 'test.rooted.tree')
options.custom_taxonomy_file = None
options.gtdbtk_classification_file = None
self.optionparser.root(options)
self.assertTrue(os.path.isfile(options.output_tree))
class TestCli(unittest.TestCase):
def setUp(self):
self.identify_dir_reference = os.path.join(
os.path.dirname(__file__), 'data/identify_dir_reference/')
self.align_dir_reference = 'tests/data/align_dir_reference/'
self.genome_dir = 'gtdbtk/tests/data/genomes/'
self.options = argparse.ArgumentParser()
self.options.batchfile = None
self.options.prefix = 'gtdbtk'
self.options.cpus = 1
self.options.extension = 'fna'
self.options.debug = False
self.options.force = False
self.options.genes = False
self.options.write_single_copy_genes = False
# align option
self.options.skip_gtdb_refs = False
self.options.taxa_filter = None
self.options.custom_msa_filters = False
self.options.skip_trimming = False
self.options.min_consensus = None
self.options.min_perc_taxa = None
self.options.skip_gtdb_refs = False
self.options.cols_per_gene = None
self.options.max_consensus = None
self.options.min_perc_aa = 50
self.options.rnd_seed = 42
# classify options
self.options.scratch_dir = None
self.options.keep_ref_red = None
self.options.pplacer_cpus = None
# infer options
self.options.prot_model = 'WAG'
self.options.no_support = False
self.options.no_gamma = True
self.version = ' unittest'
self.optionparser = OptionsParser(self.version)
logger_setup(None, "gtdbtk.log", "GTDB-Tk", self.version, True)
# self.generic_out_path = 'tests/data/results'
self.generic_out_path = tempfile.mkdtemp(prefix='gtdbtk_tmp_')
def test_identify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
ar122_marker_path = os.path.join(
self.options.out_dir,
PATH_AR122_MARKER_SUMMARY.format(prefix=self.options.prefix))
self.assertTrue(
os.path.isfile(
os.path.join(
self.options.out_dir,
PATH_BAC120_MARKER_SUMMARY.format(
prefix=self.options.prefix))))
self.assertTrue(os.path.isfile(ar122_marker_path))
results = {}
with open(ar122_marker_path, 'r') as f:
f.readline()
for line in f:
infos = line.split('\t', 1)
results[infos[0]] = infos[1]
self.assertTrue(results.get('genome_1').startswith('120\t2\t0\t'))
def test_align(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
align_options = self.options
align_options.identify_dir = self.identify_dir_reference
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(
align_options.out_dir,
PATH_AR122_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_classify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.align_dir = self.align_dir_reference
classify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify')
classify_options.recalculate_red = False
classify_options.split_tree = False
self.optionparser.classify(classify_options)
summary_fh = ClassifySummaryFileAR122(classify_options.out_dir,
classify_options.prefix)
summary_fh.read()
self.assertEqual(
'd__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium',
summary_fh.rows['genome_1'].classification)
self.assertEqual(
'd__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365',
summary_fh.rows['genome_2'].classification)
self.assertEqual(
'd__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365',
summary_fh.rows['genome_3'].classification)
def test_identify_align(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(
align_options.out_dir,
PATH_AR122_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_identify_align_classify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(
align_options.out_dir,
PATH_AR122_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.split_tree = False
classify_options.align_dir = align_options.out_dir
classify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify')
classify_options.recalculate_red = False
self.optionparser.classify(classify_options)
summary_out = os.path.join(
classify_options.out_dir,
PATH_AR122_SUMMARY_OUT.format(prefix=classify_options.prefix))
self.assertTrue(summary_out)
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 19)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_classify_wf(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
classify_wf_options = self.options
classify_wf_options.genome_dir = self.genome_dir
classify_wf_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify_wf')
self.optionparser.identify(classify_wf_options)
classify_wf_options.identify_dir = classify_wf_options.out_dir
classify_wf_options.align_dir = classify_wf_options.out_dir
classify_wf_options.taxa_filter = None
classify_wf_options.custom_msa_filters = False
classify_wf_options.min_consensus = None
classify_wf_options.min_perc_taxa = None
classify_wf_options.skip_gtdb_refs = False
classify_wf_options.cols_per_gene = None
classify_wf_options.max_consensus = None
classify_wf_options.recalculate_red = False
classify_wf_options.split_tree = False
self.optionparser.align(classify_wf_options)
self.optionparser.classify(classify_wf_options)
summary_out = os.path.join(
classify_wf_options.out_dir,
PATH_AR122_SUMMARY_OUT.format(prefix=classify_wf_options.prefix))
self.assertTrue(os.path.isfile(summary_out))
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEqual(len(infos), 19)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_infer(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
infer_options = self.options
path_user_msa = PATH_AR122_USER_MSA.format(prefix=self.options.prefix)
infer_options.msa_file = os.path.join(self.align_dir_reference,
path_user_msa)
infer_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'infer')
infer_options.gamma = False
# if not os.path.isdir(infer_options.out_dir):
# os.makedirs(infer_options.out_dir)
self.optionparser.infer(infer_options)
with open(
os.path.join(infer_options.out_dir,
PATH_TREE_LOG.format(prefix=self.options.prefix)),
'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertEqual(last_line.strip(), 'TreeCompleted')
with open(
os.path.join(
infer_options.out_dir,
PATH_UNROOTED_TREE.format(prefix=self.options.prefix)),
'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue('genome_1' in last_line)
self.assertTrue('genome_2' in last_line)
self.assertTrue('genome_3' in last_line)
def test_de_novo_wf(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
de_novo_wf_options = self.options
de_novo_wf_options.genome_dir = self.genome_dir
de_novo_wf_options.suffix = ".ar122"
de_novo_wf_options.gamma = False
de_novo_wf_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'de_novo_wf')
de_novo_wf_options.identify_dir = de_novo_wf_options.out_dir
de_novo_wf_options.msa_file = os.path.join(
de_novo_wf_options.out_dir, de_novo_wf_options.prefix +
de_novo_wf_options.suffix + ".user_msa.fasta")
self.optionparser.identify(de_novo_wf_options)
self.optionparser.align(de_novo_wf_options)
self.optionparser.infer(de_novo_wf_options)
def test_identify_gzipped_genomes(self):
""" Test that gene calling is successful when using gzipped genomes """
options = argparse.ArgumentParser()
options.genome_dir = 'tests/data/genomes_gz/'
options.cpus = 5
options.batchfile = None
options.extension = 'fna.gz'
options.write_single_copy_genes = False
options.prefix = 'gtdbtk'
options.force = None
options.genes = False
options.out_dir = self.generic_out_path
self.optionparser.identify(options)
self.assertTrue(
are_files_equal(
os.path.join(
self.identify_dir_reference,
PATH_BAC120_MARKER_SUMMARY.format(prefix='gtdbtk')),
os.path.join(
self.generic_out_path,
PATH_BAC120_MARKER_SUMMARY.format(prefix='gtdbtk')),
ignore_order=True))
self.assertTrue(
are_files_equal(
os.path.join(
self.identify_dir_reference,
PATH_AR122_MARKER_SUMMARY.format(prefix='gtdbtk')),
os.path.join(
self.generic_out_path,
PATH_AR122_MARKER_SUMMARY.format(prefix='gtdbtk')),
ignore_order=True))
self.assertTrue(
are_files_equal(
os.path.join(self.identify_dir_reference,
PATH_TLN_TABLE_SUMMARY.format(prefix='gtdbtk')),
os.path.join(self.generic_out_path,
PATH_TLN_TABLE_SUMMARY.format(prefix='gtdbtk')),
ignore_order=True))
def test_root(self):
"""Test that rooting is successful when called through the CLI"""
options = argparse.ArgumentParser()
options.input_tree = 'tests/data/pplacer_dir_reference/gtdbtk.ar122.classify.tree'
options.outgroup_taxon = 'p__Altarchaeota'
options.output_tree = os.path.join(self.generic_out_path,
'test.rooted.tree')
options.custom_taxonomy_file = None
options.gtdbtk_classification_file = None
self.optionparser.root(options)
self.assertTrue(os.path.isfile(options.output_tree))
def tearDown(self):
shutil.rmtree(self.generic_out_path)
class TestCli(unittest.TestCase):
def setUp(self):
self.identify_dir_reference = 'tests/data/identify_dir_reference/'
self.align_dir_reference = 'tests/data/align_dir_reference/'
self.genome_dir = 'gtdbtk/tests/data/genomes/'
self.options = argparse.ArgumentParser()
self.options.batchfile = None
self.options.prefix = 'gtdbtk'
self.options.cpus = 1
self.options.extension = 'fna'
self.options.debug = False
# align option
self.options.skip_gtdb_refs = False
self.options.taxa_filter = None
self.options.custom_msa_filters = False
self.options.min_consensus = None
self.options.min_perc_taxa = None
self.options.skip_gtdb_refs = False
self.options.cols_per_gene = None
self.options.max_consensus = None
self.options.min_perc_aa = 50
# classify options
self.options.scratch_dir = None
# infer options
self.options.prot_model = 'WAG'
self.options.no_support = False
self.options.no_gamma = True
self.version = ' unittest'
self.optionparser = OptionsParser(self.version)
logger_setup(None, "gtdbtk.log", "GTDB-Tk", self.version, True)
self.generic_out_path = 'tests/data/results'
def test_identify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
self.assertTrue(
os.path.isfile(
os.path.join(self.options.out_dir,
'gtdbtk_bac120_markers_summary.tsv')))
self.assertTrue(
os.path.isfile(
os.path.join(self.options.out_dir,
'gtdbtk_ar122_markers_summary.tsv')))
results = {}
with open(
os.path.join(identify_options.out_dir,
'gtdbtk_ar122_markers_summary.tsv'), 'r') as f:
f.readline()
for line in f:
infos = line.split('\t', 1)
results[infos[0]] = infos[1]
self.assertTrue(results.get('genome_1').startswith('120\t2\t0\t'))
def test_align(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
align_options = self.options
align_options.identify_dir = self.identify_dir_reference
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
self.assertTrue(
os.path.isfile(
os.path.join(align_options.out_dir,
'gtdbtk.ar122.user_msa.fasta')))
with open(
os.path.join(align_options.out_dir,
'gtdbtk.ar122.user_msa.fasta'), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_classify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.align_dir = self.align_dir_reference
classify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify')
self.optionparser.classify(classify_options)
self.assertTrue(
os.path.isfile(
os.path.join(classify_options.out_dir,
'gtdbtk.ar122.summary.tsv')))
with open(
os.path.join(classify_options.out_dir,
'gtdbtk.ar122.summary.tsv'), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 17)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_identify_align(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
self.assertTrue(
os.path.isfile(
os.path.join(align_options.out_dir,
'gtdbtk.ar122.user_msa.fasta')))
with open(
os.path.join(align_options.out_dir,
'gtdbtk.ar122.user_msa.fasta'), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_identify_align_classify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
self.assertTrue(
os.path.isfile(
os.path.join(align_options.out_dir,
'gtdbtk.ar122.user_msa.fasta')))
with open(
os.path.join(align_options.out_dir,
'gtdbtk.ar122.user_msa.fasta'), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.align_dir = align_options.out_dir
classify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify')
self.optionparser.classify(classify_options)
self.assertTrue(
os.path.isfile(
os.path.join(classify_options.out_dir,
'gtdbtk.ar122.summary.tsv')))
with open(
os.path.join(classify_options.out_dir,
'gtdbtk.ar122.summary.tsv'), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 17)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_classify_wf(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
classify_wf_options = self.options
classify_wf_options.genome_dir = self.genome_dir
classify_wf_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify_wf')
self.optionparser.identify(classify_wf_options)
classify_wf_options.identify_dir = classify_wf_options.out_dir
classify_wf_options.align_dir = classify_wf_options.out_dir
classify_wf_options.taxa_filter = None
classify_wf_options.custom_msa_filters = False
classify_wf_options.min_consensus = None
classify_wf_options.min_perc_taxa = None
classify_wf_options.skip_gtdb_refs = False
classify_wf_options.cols_per_gene = None
classify_wf_options.max_consensus = None
self.optionparser.align(classify_wf_options)
self.optionparser.classify(classify_wf_options)
self.assertTrue(
os.path.isfile(
os.path.join(classify_wf_options.out_dir,
'gtdbtk.ar122.summary.tsv')))
with open(
os.path.join(classify_wf_options.out_dir,
'gtdbtk.ar122.summary.tsv'), 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 17)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_infer(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
infer_options = self.options
infer_options.msa_file = os.path.join(self.align_dir_reference,
'gtdbtk.ar122.user_msa.fasta')
infer_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'infer')
self.optionparser.infer(infer_options)
with open(os.path.join(infer_options.out_dir, 'gtdbtk.tree.log'),
'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertEqual(last_line.strip(), 'TreeCompleted')
with open(os.path.join(infer_options.out_dir, 'gtdbtk.unrooted.tree'),
'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue('genome_1' in last_line)
self.assertTrue('genome_2' in last_line)
self.assertTrue('genome_3' in last_line)
def test_de_novo_wf(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
de_novo_wf_options = self.options
de_novo_wf_options.genome_dir = self.genome_dir
de_novo_wf_options.suffix = ".ar122"
de_novo_wf_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'de_novo_wf')
de_novo_wf_options.identify_dir = de_novo_wf_options.out_dir
de_novo_wf_options.msa_file = os.path.join(
de_novo_wf_options.out_dir, de_novo_wf_options.prefix +
de_novo_wf_options.suffix + ".user_msa.fasta")
self.optionparser.identify(de_novo_wf_options)
self.optionparser.align(de_novo_wf_options)
self.optionparser.infer(de_novo_wf_options)
def tearDown(self):
shutil.rmtree(self.generic_out_path)
class TestCli(unittest.TestCase):
def setUp(self):
self.identify_dir_reference = os.path.join(
os.path.dirname(__file__), 'data/identify_dir_reference/')
self.align_dir_reference = 'tests/data/align_dir_reference/'
self.genome_dir = 'gtdbtk/tests/data/genomes/'
self.options = argparse.ArgumentParser()
self.options.batchfile = None
self.options.prefix = 'gtdbtk'
self.options.cpus = 1
self.options.extension = 'fna'
self.options.debug = False
self.options.force = False
# align option
self.options.skip_gtdb_refs = False
self.options.taxa_filter = None
self.options.custom_msa_filters = False
self.options.skip_trimming = False
self.options.min_consensus = None
self.options.min_perc_taxa = None
self.options.skip_gtdb_refs = False
self.options.cols_per_gene = None
self.options.max_consensus = None
self.options.min_perc_aa = 50
self.options.rnd_seed = 42
# classify options
self.options.scratch_dir = None
self.options.keep_ref_red = None
# infer options
self.options.prot_model = 'WAG'
self.options.no_support = False
self.options.no_gamma = True
self.version = ' unittest'
self.optionparser = OptionsParser(self.version)
logger_setup(None, "gtdbtk.log", "GTDB-Tk", self.version, True)
# self.generic_out_path = 'tests/data/results'
self.generic_out_path = '/tmp/GTDBTk/tests'
def test_identify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
ar122_marker_path = os.path.join(
self.options.out_dir,
PATH_AR122_MARKER_SUMMARY.format(prefix=self.options.prefix))
self.assertTrue(
os.path.isfile(
os.path.join(
self.options.out_dir,
PATH_BAC120_MARKER_SUMMARY.format(
prefix=self.options.prefix))))
self.assertTrue(os.path.isfile(ar122_marker_path))
results = {}
with open(ar122_marker_path, 'r') as f:
f.readline()
for line in f:
infos = line.split('\t', 1)
results[infos[0]] = infos[1]
self.assertTrue(results.get('genome_1').startswith('120\t2\t0\t'))
def test_align(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
align_options = self.options
align_options.identify_dir = self.identify_dir_reference
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(
align_options.out_dir,
PATH_AR122_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_classify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.align_dir = self.align_dir_reference
classify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify')
self.optionparser.classify(classify_options)
summary_out = os.path.join(
classify_options.out_dir,
PATH_AR122_SUMMARY_OUT.format(prefix=classify_options.prefix))
self.assertTrue(os.path.isfile(summary_out))
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 18)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_identify_align(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(
align_options.out_dir,
PATH_AR122_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
def test_identify_align_classify(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
identify_options = self.options
identify_options.genome_dir = self.genome_dir
identify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
self.optionparser.identify(identify_options)
align_options = self.options
align_options.identify_dir = os.path.join(self.generic_out_path,
tmp_folder, 'identify')
align_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'align')
self.optionparser.align(align_options)
path_user_msa = os.path.join(
align_options.out_dir,
PATH_AR122_USER_MSA.format(prefix=align_options.prefix))
self.assertTrue(os.path.isfile(path_user_msa))
with open(path_user_msa, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue(len(last_line) > 4500)
self.assertTrue(len(last_line) < 5500)
self.assertTrue('-' in last_line)
self.assertFalse(any(char.isdigit() for char in last_line))
classify_options = self.options
classify_options.genome_dir = self.genome_dir
classify_options.align_dir = align_options.out_dir
classify_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify')
self.optionparser.classify(classify_options)
summary_out = os.path.join(
classify_options.out_dir,
PATH_AR122_SUMMARY_OUT.format(prefix=classify_options.prefix))
self.assertTrue(summary_out)
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 18)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_classify_wf(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
classify_wf_options = self.options
classify_wf_options.genome_dir = self.genome_dir
classify_wf_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'classify_wf')
self.optionparser.identify(classify_wf_options)
classify_wf_options.identify_dir = classify_wf_options.out_dir
classify_wf_options.align_dir = classify_wf_options.out_dir
classify_wf_options.taxa_filter = None
classify_wf_options.custom_msa_filters = False
classify_wf_options.min_consensus = None
classify_wf_options.min_perc_taxa = None
classify_wf_options.skip_gtdb_refs = False
classify_wf_options.cols_per_gene = None
classify_wf_options.max_consensus = None
self.optionparser.align(classify_wf_options)
self.optionparser.classify(classify_wf_options)
summary_out = os.path.join(
classify_wf_options.out_dir,
PATH_AR122_SUMMARY_OUT.format(prefix=classify_wf_options.prefix))
self.assertTrue(os.path.isfile(summary_out))
with open(summary_out, 'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
infos = last_line.split('\t')
self.assertEquals(len(infos), 18)
self.assertTrue(infos[1].startswith('d__Archaea'))
def test_infer(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
infer_options = self.options
path_user_msa = PATH_AR122_USER_MSA.format(prefix=self.options.prefix)
infer_options.msa_file = os.path.join(self.align_dir_reference,
path_user_msa)
infer_options.out_dir = os.path.join(self.generic_out_path, tmp_folder,
'infer')
# if not os.path.isdir(infer_options.out_dir):
# os.makedirs(infer_options.out_dir)
self.optionparser.infer(infer_options)
with open(
os.path.join(infer_options.out_dir,
PATH_TREE_LOG.format(prefix=self.options.prefix)),
'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertEqual(last_line.strip(), 'TreeCompleted')
with open(
os.path.join(
infer_options.out_dir,
PATH_UNROOTED_TREE.format(prefix=self.options.prefix)),
'r') as f:
lines = f.read().splitlines()
last_line = lines[-1]
self.assertTrue('genome_1' in last_line)
self.assertTrue('genome_2' in last_line)
self.assertTrue('genome_3' in last_line)
def test_de_novo_wf(self):
tmp_folder = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for _ in range(10))
de_novo_wf_options = self.options
de_novo_wf_options.genome_dir = self.genome_dir
de_novo_wf_options.suffix = ".ar122"
de_novo_wf_options.out_dir = os.path.join(self.generic_out_path,
tmp_folder, 'de_novo_wf')
de_novo_wf_options.identify_dir = de_novo_wf_options.out_dir
de_novo_wf_options.msa_file = os.path.join(
de_novo_wf_options.out_dir, de_novo_wf_options.prefix +
de_novo_wf_options.suffix + ".user_msa.fasta")
self.optionparser.identify(de_novo_wf_options)
self.optionparser.align(de_novo_wf_options)
self.optionparser.infer(de_novo_wf_options)
def tearDown(self):
shutil.rmtree(self.generic_out_path)
