def setUp(self):
"""Define some sample data that will be used by the tests."""
self.res1 = RichnessEstimatesResults()
self.res2 = RichnessEstimatesResults()
self.res2.addSample('S2', 52)
self.res2.addSampleEstimate('S2', 1, 3, 0.4, 2.5, 3.5)
self.res2.addSample('S1', 42)
self.res2.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 20, 30, 3.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
def setUp(self):
"""Define some sample data that will be used by the tests."""
self.res1 = RichnessEstimatesResults()
self.res2 = RichnessEstimatesResults()
self.res2.addSample('S2', 52)
self.res2.addSampleEstimate('S2', 1, 3, 0.4, 2.5, 3.5)
self.res2.addSample('S1', 42)
self.res2.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 20, 30, 3.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
def test_toTable(self):
"""Test writing results container to a table."""
# Empty results.
out_f = StringIO()
self.res1.toTable(out_f)
self.assertEqual(
out_f.getvalue(),
"SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)\n")
out_f.close()
# Results with multiple samples.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t5\t21\t1.5\t2.5\t3.5
S1\t10\t20\t2.5\t2.5\t3.5
S1\t20\t30\t3.5\t2.5\t3.5
S2\t1\t3\t0.4\t2.5\t3.5
"""
out_f = StringIO()
self.res2.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Custom header.
exp = """foo\tbar\tbaz\tbazaar\tbazaaar\tbazaaaar
S1\t5\t21\t1.5\t2.5\t3.5
"""
out_f = StringIO()
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
self.res1.toTable(
out_f,
header=['foo', 'bar', 'baz', 'bazaar', 'bazaaar', 'bazaaaar'])
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Invalid header.
with self.assertRaises(ValueError):
out_f = StringIO()
self.res1.toTable(out_f, header=['foo'])
# Cells with None as their value.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t43\tN/A\tN/A\tN/A\tN/A
"""
out_f = StringIO()
res = RichnessEstimatesResults()
res.addSample('S1', 42)
res.addSampleEstimate('S1', 43, None, None, None, None)
res.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
def test_toTable(self):
"""Test writing results container to a table."""
# Empty results.
out_f = StringIO()
self.res1.toTable(out_f)
self.assertEqual(out_f.getvalue(),
"SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)\n")
out_f.close()
# Results with multiple samples.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t5\t21\t1.5\t2.5\t3.5
S1\t10\t20\t2.5\t2.5\t3.5
S1\t20\t30\t3.5\t2.5\t3.5
S2\t1\t3\t0.4\t2.5\t3.5
"""
out_f = StringIO()
self.res2.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Custom header.
exp = """foo\tbar\tbaz\tbazaar\tbazaaar\tbazaaaar
S1\t5\t21\t1.5\t2.5\t3.5
"""
out_f = StringIO()
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
self.res1.toTable(out_f,
header=['foo', 'bar', 'baz', 'bazaar', 'bazaaar', 'bazaaaar'])
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Invalid header.
with self.assertRaises(ValueError):
out_f = StringIO()
self.res1.toTable(out_f, header=['foo'])
# Cells with None as their value.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t43\tN/A\tN/A\tN/A\tN/A
"""
out_f = StringIO()
res = RichnessEstimatesResults()
res.addSample('S1', 42)
res.addSampleEstimate('S1', 43, None, None, None, None)
res.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
class RichnessEstimatesResultsTests(TestCase):
"""Tests for the RichnessEstimatesResults class."""
def setUp(self):
"""Define some sample data that will be used by the tests."""
self.res1 = RichnessEstimatesResults()
self.res2 = RichnessEstimatesResults()
self.res2.addSample('S2', 52)
self.res2.addSampleEstimate('S2', 1, 3, 0.4, 2.5, 3.5)
self.res2.addSample('S1', 42)
self.res2.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 20, 30, 3.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
def test_constructor(self):
"""Test instantiating a RichnessEstimatesResults instance."""
self.assertTrue(isinstance(self.res1, RichnessEstimatesResults))
self.assertEqual(self.res1.getSampleCount(), 0)
def test_getSampleCount(self):
"""Test getting the number of samples in the results container."""
self.assertEqual(self.res1.getSampleCount(), 0)
self.res1.addSample('S1', 42)
self.assertEqual(self.res1.getSampleCount(), 1)
self.res1.addSample('S2', 43)
self.assertEqual(self.res1.getSampleCount(), 2)
def test_getReferenceIndividualCount(self):
"""Test getting the original number of individuals in a sample."""
with self.assertRaises(ValueError):
self.res1.getReferenceIndividualCount('S1')
self.res1.addSample('S1', 42)
self.assertEqual(self.res1.getReferenceIndividualCount('S1'), 42)
def test_getEstimates(self):
"""Test getting the estimates for a sample."""
with self.assertRaises(ValueError):
self.res1.getEstimates('S1')
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 15, 30, 4.75, 2.5, 3.5)
self.res1.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.assertFloatEqual(self.res1.getEstimates('S1'),
[(10, 20, 2.5, 2.5, 3.5),
(15, 30, 4.75, 2.5, 3.5)])
def test_addSample(self):
"""Test adding a new sample to the results container."""
self.res1.addSample('S1', 42)
self.assertEqual(self.res1.getSampleCount(), 1)
self.assertEqual(self.res1.getReferenceIndividualCount('S1'), 42)
with self.assertRaises(ValueError):
self.res1.addSample('S1', 45)
def test_addSampleEstimate(self):
"""Test adding a new estimate for a sample."""
with self.assertRaises(ValueError):
self.res1.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.assertFloatEqual(self.res1.getEstimates('S1'),
[(10, 20, 2.5, 2.5, 3.5)])
with self.assertRaises(ValueError):
self.res1.addSampleEstimate('S1', 10, 35, 0.002, 2.5, 3.5)
def test_toTable(self):
"""Test writing results container to a table."""
# Empty results.
out_f = StringIO()
self.res1.toTable(out_f)
self.assertEqual(
out_f.getvalue(),
"SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)\n")
out_f.close()
# Results with multiple samples.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t5\t21\t1.5\t2.5\t3.5
S1\t10\t20\t2.5\t2.5\t3.5
S1\t20\t30\t3.5\t2.5\t3.5
S2\t1\t3\t0.4\t2.5\t3.5
"""
out_f = StringIO()
self.res2.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Custom header.
exp = """foo\tbar\tbaz\tbazaar\tbazaaar\tbazaaaar
S1\t5\t21\t1.5\t2.5\t3.5
"""
out_f = StringIO()
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
self.res1.toTable(
out_f,
header=['foo', 'bar', 'baz', 'bazaar', 'bazaaar', 'bazaaaar'])
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Invalid header.
with self.assertRaises(ValueError):
out_f = StringIO()
self.res1.toTable(out_f, header=['foo'])
# Cells with None as their value.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t43\tN/A\tN/A\tN/A\tN/A
"""
out_f = StringIO()
res = RichnessEstimatesResults()
res.addSample('S1', 42)
res.addSampleEstimate('S1', 43, None, None, None, None)
res.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
class RichnessEstimatesResultsTests(TestCase):
"""Tests for the RichnessEstimatesResults class."""
def setUp(self):
"""Define some sample data that will be used by the tests."""
self.res1 = RichnessEstimatesResults()
self.res2 = RichnessEstimatesResults()
self.res2.addSample('S2', 52)
self.res2.addSampleEstimate('S2', 1, 3, 0.4, 2.5, 3.5)
self.res2.addSample('S1', 42)
self.res2.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 20, 30, 3.5, 2.5, 3.5)
self.res2.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
def test_constructor(self):
"""Test instantiating a RichnessEstimatesResults instance."""
self.assertTrue(isinstance(self.res1, RichnessEstimatesResults))
self.assertEqual(self.res1.getSampleCount(), 0)
def test_getSampleCount(self):
"""Test getting the number of samples in the results container."""
self.assertEqual(self.res1.getSampleCount(), 0)
self.res1.addSample('S1', 42)
self.assertEqual(self.res1.getSampleCount(), 1)
self.res1.addSample('S2', 43)
self.assertEqual(self.res1.getSampleCount(), 2)
def test_getReferenceIndividualCount(self):
"""Test getting the original number of individuals in a sample."""
with self.assertRaises(ValueError):
self.res1.getReferenceIndividualCount('S1')
self.res1.addSample('S1', 42)
self.assertEqual(self.res1.getReferenceIndividualCount('S1'), 42)
def test_getEstimates(self):
"""Test getting the estimates for a sample."""
with self.assertRaises(ValueError):
self.res1.getEstimates('S1')
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 15, 30, 4.75, 2.5, 3.5)
self.res1.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.assertFloatEqual(self.res1.getEstimates('S1'),
[(10, 20, 2.5, 2.5, 3.5), (15, 30, 4.75, 2.5, 3.5)])
def test_addSample(self):
"""Test adding a new sample to the results container."""
self.res1.addSample('S1', 42)
self.assertEqual(self.res1.getSampleCount(), 1)
self.assertEqual(self.res1.getReferenceIndividualCount('S1'), 42)
with self.assertRaises(ValueError):
self.res1.addSample('S1', 45)
def test_addSampleEstimate(self):
"""Test adding a new estimate for a sample."""
with self.assertRaises(ValueError):
self.res1.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 10, 20, 2.5, 2.5, 3.5)
self.assertFloatEqual(self.res1.getEstimates('S1'),
[(10, 20, 2.5, 2.5, 3.5)])
with self.assertRaises(ValueError):
self.res1.addSampleEstimate('S1', 10, 35, 0.002, 2.5, 3.5)
def test_toTable(self):
"""Test writing results container to a table."""
# Empty results.
out_f = StringIO()
self.res1.toTable(out_f)
self.assertEqual(out_f.getvalue(),
"SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)\n")
out_f.close()
# Results with multiple samples.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t5\t21\t1.5\t2.5\t3.5
S1\t10\t20\t2.5\t2.5\t3.5
S1\t20\t30\t3.5\t2.5\t3.5
S2\t1\t3\t0.4\t2.5\t3.5
"""
out_f = StringIO()
self.res2.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Custom header.
exp = """foo\tbar\tbaz\tbazaar\tbazaaar\tbazaaaar
S1\t5\t21\t1.5\t2.5\t3.5
"""
out_f = StringIO()
self.res1.addSample('S1', 42)
self.res1.addSampleEstimate('S1', 5, 21, 1.5, 2.5, 3.5)
self.res1.toTable(out_f,
header=['foo', 'bar', 'baz', 'bazaar', 'bazaaar', 'bazaaaar'])
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
# Invalid header.
with self.assertRaises(ValueError):
out_f = StringIO()
self.res1.toTable(out_f, header=['foo'])
# Cells with None as their value.
exp = """SampleID\tSize\tEstimate\tStd Err\tCI (lower)\tCI (upper)
S1\t43\tN/A\tN/A\tN/A\tN/A
"""
out_f = StringIO()
res = RichnessEstimatesResults()
res.addSample('S1', 42)
res.addSampleEstimate('S1', 43, None, None, None, None)
res.toTable(out_f)
self.assertEqual(out_f.getvalue(), exp)
out_f.close()
