def mothur_from_file(file):
app = Mothur(InputHandler='_input_as_lines')
result = app(file)
# Force evaluation, so we can safely clean up files
otus = list(parse_otu_list(result['otu list']))
result.cleanUp()
return otus
def mothur_from_file(file):
app = Mothur(InputHandler='_input_as_lines')
result = app(file)
# Force evaluation, so we can safely clean up files
otus = list(parse_otu_list(result['otu list']))
result.cleanUp()
return otus
def test_parse_otu_list(self):
observed = list(parse_otu_list(StringIO(mothur_output)))
expected = [
(0.0, [['cccccc'], ['bbbbbb'], ['aaaaaa']]),
(0.62, [['bbbbbb', 'cccccc'], ['aaaaaa']]),
(0.67000000000000004, [['aaaaaa', 'bbbbbb', 'cccccc']])
]
self.assertEqual(observed, expected)
def test_parse_otu_list(self):
observed = list(parse_otu_list(StringIO(mothur_output)))
expected = [
(0.0, [['cccccc'], ['bbbbbb'], ['aaaaaa']]),
(0.62, [['bbbbbb', 'cccccc'], ['aaaaaa']]),
(0.67000000000000004, [['aaaaaa', 'bbbbbb', 'cccccc']])
]
self.assertEqual(observed, expected)
