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)