def test_get_process_target_gene_cmd(self):
preprocessed_data = PreprocessedData(1)
params = ProcessedSortmernaParams(1)
obs_cmd, obs_output_dir = _get_process_target_gene_cmd(
preprocessed_data, params)
_, ref_dir = get_mountpoint('reference')[0]
_, preprocessed_dir = get_mountpoint('preprocessed_data')[0]
exp_cmd = ("pick_closed_reference_otus.py -i {}1_seqs.fna -r "
"{}GreenGenes_13_8_97_otus.fasta -o {} -p placeholder -t "
"{}GreenGenes_13_8_97_otu_taxonomy.txt".format(
preprocessed_dir, ref_dir, obs_output_dir, ref_dir))
obs_tokens = obs_cmd.split()[::-1]
exp_tokens = exp_cmd.split()[::-1]
self.assertEqual(len(obs_tokens), len(exp_tokens))
while obs_tokens:
o_t = obs_tokens.pop()
e_t = exp_tokens.pop()
if o_t == '-p':
# skip parameters file
obs_tokens.pop()
exp_tokens.pop()
else:
self.assertEqual(o_t, e_t)
def test_generate_param_str(self):
params = ProcessedSortmernaParams(1)
obs = generate_param_str(params)
exp = ("<b>Reference:</b> Greengenes 13_8<br/>"
"<b>similarity:</b> 0.97<br/>"
"<b>sortmerna_e_value:</b> 1.0<br/>"
"<b>sortmerna_max_pos:</b> 10000<br/>"
"<b>threads:</b> 1<br/>"
"<b>sortmerna_coverage:</b> 0.97")
self.assertEqual(obs, exp)
def test_to_file(self):
params = ProcessedSortmernaParams(1)
fd, fp = mkstemp()
close(fd)
with open(fp, 'w') as f:
params.to_file(f)
with open(fp, 'U') as f:
obs = f.read()
self.assertEqual(obs, EXP_SMR_PARAMS_FILE)
def test_insert_processed_data_target_gene(self):
fd, fna_fp = mkstemp(suffix='_seqs.fna')
close(fd)
fd, qual_fp = mkstemp(suffix='_seqs.qual')
close(fd)
filepaths = [
(fna_fp, convert_to_id('preprocessed_fasta', 'filepath_type')),
(qual_fp, convert_to_id('preprocessed_fastq', 'filepath_type'))
]
preprocessed_data = PreprocessedData.create(
Study(1),
"preprocessed_sequence_illumina_params",
1,
filepaths,
data_type="18S")
params = ProcessedSortmernaParams(1)
pick_dir = mkdtemp()
path_builder = partial(join, pick_dir)
db_path_builder = partial(join, get_mountpoint('processed_data')[0][1])
# Create a placeholder for the otu table
with open(path_builder('otu_table.biom'), 'w') as f:
f.write('\n')
# Create a placeholder for the directory
mkdir(path_builder('sortmerna_picked_otus'))
# Create the log file
fd, fp = mkstemp(dir=pick_dir, prefix='log_', suffix='.txt')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
_insert_processed_data_target_gene(preprocessed_data, params, pick_dir)
new_id = get_count('qiita.processed_data')
# Check that the files have been copied
db_files = [
db_path_builder("%s_otu_table.biom" % new_id),
db_path_builder("%s_sortmerna_picked_otus" % new_id),
db_path_builder("%s_%s" % (new_id, basename(fp)))
]
for fp in db_files:
self.assertTrue(exists(fp))
# Check that a new preprocessed data has been created
self.assertTrue(
self.conn_handler.execute_fetchone(
"SELECT EXISTS(SELECT * FROM qiita.processed_data WHERE "
"processed_data_id=%s)", (new_id, ))[0])
def test_to_str(self):
params = ProcessedSortmernaParams(1)
obs = params.to_str()
exp = ("--similarity 0.97 --sortmerna_coverage 0.97 "
"--sortmerna_e_value 1.0 --sortmerna_max_pos 10000 --threads 1")
self.assertEqual(obs, exp)
