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#!/usr/bin/env python
#file cogent.parse.mothur.py
__author__ = "Kyle Bittinger"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Kyle Bittinger"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Prototype"
from cStringIO import StringIO
from cogent.util.unit_test import TestCase, main
from cogent.parse.mothur import parse_otu_list
class FunctionTests(TestCase):
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)
mothur_output = """\
unique 3 cccccc bbbbbb aaaaaa
0.62 2 bbbbbb,cccccc aaaaaa
0.67 1 aaaaaa,bbbbbb,cccccc
"""
if __name__ == '__main__':
main()
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