Exemplo n.º 1
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 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)
Exemplo n.º 2
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 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)
Exemplo n.º 3
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 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)