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#!/usr/bin/env python
#file test_parse.py
from numpy import array
from cogent.util.unit_test import TestCase, main
from cogent.maths.stats.rarefaction import subsample, naive_histogram, wrap_numpy_histogram, \
rarefaction
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def test_subsample(self):
"""subsample should return a random subsample of a vector"""
a = array([0,5,0])
self.assertEqual(subsample(a,5), array([0,5,0]))
self.assertEqual(subsample(a,2), array([0,2,0]))
b = array([2,0,1])
obs = subsample(b,2)
assert (obs == array([1,0,1])).all() or (obs == array([2,0,0])).all()
def test_naive_histogram(self):
"""naive_histogram should produce expected result"""
vals = array([1,0,0,3])
self.assertEqual(naive_histogram(vals), array([2,1,0,1]))
self.assertEqual(naive_histogram(vals, 4), array([2,1,0,1,0]))
def test_wrap_numpy_histogram(self):
"""wrap_numpy_histogram should provide expected result"""
vals = array([1,0,0,3])
h_f = wrap_numpy_histogram(3)
self.assertEqual(h_f(vals), array([2,1,0,1]))
h_f = wrap_numpy_histogram(4)
self.assertEqual(h_f(vals, 4), array([2,1,0,1,0]))
def test_rarefaction(self):
"""rarefaction should produce expected curve"""
vals = array([5,0,0,3,0,10], dtype=int)
res = [r.copy() for r in rarefaction(vals, stride=1)]
self.assertEqual(len(res), 18)
for i, r in enumerate(res):
self.assertEqual(r.sum(), i+1)
#make sure we didn't add any bad counts
for pos in [1,2,4]:
self.assertEqual(r[pos], 0)
#when we get to end should recapture orig vals
self.assertEqual(r, vals)
res = [r.copy() for r in rarefaction(vals, stride=3)]
self.assertEqual(len(res), 6)
for i, r in enumerate(res):
self.assertEqual(r.sum(), 3*(i+1))
#make sure we didn't add any bad counts
for pos in [1,2,4]:
self.assertEqual(r[pos], 0)
#when we get to end should recapture orig vals
self.assertEqual(r, vals)
#repeat everything above using alt. input format
orig_vals = vals.copy()
vals = array([0,0,0,0,0,3,3,3,5,5,5,5,5,5,5,5,5,5], dtype=int)
res = [r.copy() for r in rarefaction(vals, stride=1, is_counts=False)]
self.assertEqual(len(res), 18)
for i, r in enumerate(res):
self.assertEqual(r.sum(), i+1)
#make sure we didn't add any bad counts
for pos in [1,2,4]:
self.assertEqual(r[pos], 0)
#when we get to end should recapture orig vals
self.assertEqual(r, orig_vals)
res = [r.copy() for r in rarefaction(vals, stride=3, is_counts=False)]
self.assertEqual(len(res), 6)
for i, r in enumerate(res):
self.assertEqual(r.sum(), 3*(i+1))
#make sure we didn't add any bad counts
for pos in [1,2,4]:
self.assertEqual(r[pos], 0)
#when we get to end should recapture orig vals
self.assertEqual(r, orig_vals)
if __name__ =='__main__':
main()
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