Python parse_otu_list Examples

Example #1

File: mothur.py Project: cxhernandez/pycogent

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

Example #2

File: mothur.py Project: cxhernandez/pycogent

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

Example #3

File: test_mothur.py Project: GavinHuttley/pycogent

 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)

Example #4

 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)