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#!/usr/bin/env python
"""Tests for computing shared phylotypes."""
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jose Clemente"
__email__ = "jose.clemente@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from qiime.parse import parse_otu_table
from qiime.shared_phylotypes import _calc_shared_phylotypes_pairwise,\
_calc_shared_phylotypes_multiple, calc_shared_phylotypes
class Test_shared_phylotypes(TestCase):
def setUp(self):
self.otu_table_as_string = ["#Test otu table",
"\t".join(["#OTU ID","S1","S2","S3"]),
"\t".join(["0", "1" ,"0" ,"2" ]),
"\t".join(["1", "1" ,"2" ,"0" ]),
"\t".join(["2", "1" ,"0" ,"0" ]),
"\t".join(["3", "1" ,"0" ,"2" ]),
"\t".join(["4", "1" ,"1" ,"2" ])]
_, _, self.otu_table, _ = parse_otu_table(self.otu_table_as_string)
def test_calc_shared_phylotypes_pairwise(self):
"""_calc_shared_phylotypes_pairwise works as expected"""
self.assertEqual(_calc_shared_phylotypes_pairwise(self.otu_table, 0, 0), 5)
self.assertEqual(_calc_shared_phylotypes_pairwise(self.otu_table, 0, 1), 2)
self.assertEqual(_calc_shared_phylotypes_pairwise(self.otu_table, 0, 2), 3)
self.assertEqual(_calc_shared_phylotypes_pairwise(self.otu_table, 2, 2), 3)
def test_calc_shared_phylotypes_multiple(self):
"""_calc_shared_phylotypes_multiple works as expected"""
#test for <2 idxes
self.assertRaises(ValueError, _calc_shared_phylotypes_multiple, self.otu_table, [])
self.assertRaises(ValueError, _calc_shared_phylotypes_multiple, self.otu_table, [0])
#test that func is identical to _calc_shared_phylotypes_pairwise with 2 idx
self.assertEqual(_calc_shared_phylotypes_multiple(self.otu_table, [0, 0]), 5)
self.assertEqual(_calc_shared_phylotypes_multiple(self.otu_table, [0, 1]), 2)
self.assertEqual(_calc_shared_phylotypes_multiple(self.otu_table, [0, 2]), 3)
self.assertEqual(_calc_shared_phylotypes_multiple(self.otu_table, [2, 2]), 3)
# works with more than 2 samples
self.assertEqual(_calc_shared_phylotypes_multiple(self.otu_table, [0,1,2]), 1)
def test_calc_shared_phylotypes(self):
"""calc_shared_phylotypes computes correct matrix"""
observed = calc_shared_phylotypes(iter(self.otu_table_as_string))
expected = """\tS1\tS2\tS3
S1\t5\t2\t3
S2\t2\t2\t1
S3\t3\t1\t3\n"""
self.assertEqual(observed, expected)
if __name__ == "__main__":
main()
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