def test_format_shogun_params(self): obs = _format_params(self.params, SHOGUN_PARAMS) exp = { 'database': join(self.db_path, 'shogun'), 'aligner': 'bowtie2', 'threads': 1 } self.assertEqual(obs, exp)
def test_format_shogun_params(self): obs = _format_params(self.params, SHOGUN_PARAMS) exp = { 'database': join(self.db_path, 'rep82'), 'aligner': 'bowtie2', 'threads': 5, 'percent_id': 0.95, 'capitalist': False } self.assertEqual(obs, exp)
def test_generate_shogun_align_commands(self): out_dir = self.out_dir with TemporaryDirectory(dir=out_dir, prefix='shogun_') as temp_dir: exp_cmd = [('shogun align --aligner bowtie2 --threads 1 ' '--database %sshogun --input %s/combined.fna ' '--output %s') % (self.db_path, temp_dir, temp_dir)] params = _format_params(self.params, SHOGUN_PARAMS) obs_cmd = generate_shogun_align_commands( join(temp_dir, 'combined.fna'), temp_dir, params) self.assertEqual(obs_cmd, exp_cmd)
def test_generate_shogun_redist_commands(self): out_dir = self.out_dir with TemporaryDirectory(dir=out_dir, prefix='shogun_') as temp_dir: exp_cmd = [('shogun redistribute ' '--database %sshogun --level species --input %s ' '--output %s') % (self.db_path, join(temp_dir, 'profile.tsv'), join(temp_dir, 'profile.redist.species.tsv'))] profile_dir = join(temp_dir, 'profile.tsv') params = _format_params(self.params, SHOGUN_PARAMS) obs_cmd, output = generate_shogun_redist_commands( profile_dir, temp_dir, params, 'species') self.assertEqual(obs_cmd, exp_cmd)
def test_generate_shogun_assign_taxonomy_commands(self): out_dir = self.out_dir with TemporaryDirectory(dir=out_dir, prefix='shogun_') as temp_dir: exp_cmd = [('shogun assign_taxonomy --aligner bowtie2 ' '--database %sshogun --input %s/alignment.bowtie2.sam ' '--output %s/profile.tsv') % (self.db_path, temp_dir, temp_dir)] exp_output_fp = join(temp_dir, 'profile.tsv') params = _format_params(self.params, SHOGUN_PARAMS) obs_cmd, obs_output_fp = generate_shogun_assign_taxonomy_commands( temp_dir, params) self.assertEqual(obs_cmd, exp_cmd) self.assertEqual(obs_output_fp, exp_output_fp)