def test_compile_mothur_script(self):
"""Mothur._compile_mothur_script() should return valid Mothur script"""
app = Mothur()
app._input_filename = 'test.fasta'
observed_script = app._compile_mothur_script()
expected_script = (
'#unique.seqs(fasta=test.fasta); '
'dist.seqs(fasta=test.unique.fasta); '
'read.dist(column=test.unique.dist, name=test.names); '
'cluster(method=furthest)')
self.assertEqual(observed_script, expected_script)
def test_get_help(self):
"""Mothur.getHelp() should return help string"""
expected_help = (
'See manual, available on the MOTHUR wiki:\n'
'http://schloss.micro.umass.edu/mothur/'
)
self.assertEqual(Mothur.getHelp(), expected_help)
def test_get_result_paths(self):
"""Mothur._get_result_paths() should guess correct output paths"""
app = Mothur()
app._input_filename = 'test.fasta'
observed_paths = {
'distance matrix': app._derive_dist_path(),
'otu list': app._derive_list_path(),
'rank abundance': app._derive_rank_abundance_path(),
'species abundance': app._derive_species_abundance_path(),
'unique names': app._derive_names_path(),
'unique seqs': app._derive_unique_path(),
}
expected_paths = {
'distance matrix': 'test.unique.dist',
'otu list': 'test.unique.fn.list',
'rank abundance': 'test.unique.fn.rabund',
'species abundance': 'test.unique.fn.sabund',
'unique names': 'test.names',
'unique seqs': 'test.unique.fasta',
}
self.assertEqual(observed_paths, expected_paths)