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'))