def test_generate_pick_closed_reference_otus_cmd_valueerror(self):
filepaths = [('/directory/seqs.log', 'log'),
('/directory/seqs.demux', 'preprocessed_demux')]
parameters = {
"reference": 1, "sortmerna_e_value": 1, "sortmerna_max_pos": 10000,
"similarity": 0.97, "sortmerna_coverage": 0.97, "threads": 1,
"input_data": 1}
reference_fps = [('/directory/refseqs.fna', 'reference_seqs'),
('/directory/reftax.txt', 'reference_tax'),
('/directory/reftree.tre', 'reference_tree')]
output_dir = "/directory/out"
with self.assertRaises(ValueError):
generate_pick_closed_reference_otus_cmd(
filepaths, output_dir, parameters, reference_fps)
def test_generate_pick_closed_reference_otus_cmd(self):
output_dir = mkdtemp()
self._clean_up_files.append(output_dir)
filepaths = [('/directory/seqs.fna', 'preprocessed_fasta'),
('/directory/seqs.demux', 'preprocessed_demux')]
parameters = {
"reference": 1,
"sortmerna_e_value": 1,
"sortmerna_max_pos": 10000,
"similarity": 0.97,
"sortmerna_coverage": 0.97,
"threads": 1,
"input_data": 1
}
reference_fps = [('/directory/refseqs.fna', 'reference_seqs'),
('/directory/reftax.txt', 'reference_tax'),
('/directory/reftree.tre', 'reference_tree')]
obs, obs_dir = generate_pick_closed_reference_otus_cmd(
filepaths, output_dir, parameters, reference_fps)
exp = ("pick_closed_reference_otus.py -i /directory/seqs.fna "
"-r /directory/refseqs.fna -o {0}/cr_otus -p {0}/cr_params.txt "
"-t /directory/reftax.txt".format(output_dir))
self.assertEqual(obs, exp)
self.assertEqual(obs_dir, join(output_dir, 'cr_otus'))
def test_generate_pick_closed_reference_otus_cmd_valueerror(self):
filepaths = [('/directory/seqs.log', 'log'),
('/directory/seqs.demux', 'preprocessed_demux')]
parameters = {
"reference": 1,
"sortmerna_e_value": 1,
"sortmerna_max_pos": 10000,
"similarity": 0.97,
"sortmerna_coverage": 0.97,
"threads": 1,
"input_data": 1
}
reference_fps = [('/directory/refseqs.fna', 'reference_seqs'),
('/directory/reftax.txt', 'reference_tax'),
('/directory/reftree.tre', 'reference_tree')]
output_dir = "/directory/out"
with self.assertRaises(ValueError):
generate_pick_closed_reference_otus_cmd(filepaths, output_dir,
parameters, reference_fps)
def test_generate_pick_closed_reference_otus_cmd(self):
output_dir = mkdtemp()
self._clean_up_files.append(output_dir)
filepaths = [('/directory/seqs.fna', 'preprocessed_fasta'),
('/directory/seqs.demux', 'preprocessed_demux')]
parameters = {
"reference": 1, "sortmerna_e_value": 1, "sortmerna_max_pos": 10000,
"similarity": 0.97, "sortmerna_coverage": 0.97, "threads": 1,
"input_data": 1}
reference_fps = [('/directory/refseqs.fna', 'reference_seqs'),
('/directory/reftax.txt', 'reference_tax'),
('/directory/reftree.tre', 'reference_tree')]
obs, obs_dir = generate_pick_closed_reference_otus_cmd(
filepaths, output_dir, parameters, reference_fps)
exp = ("pick_closed_reference_otus.py -i /directory/seqs.fna "
"-r /directory/refseqs.fna -o {0}/cr_otus -p {0}/cr_params.txt "
"-t /directory/reftax.txt".format(output_dir))
self.assertEqual(obs, exp)
self.assertEqual(obs_dir, join(output_dir, 'cr_otus'))
