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#!/usr/bin/env python
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["justin kuczynski", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
"""Contains tests for producing rarefied OTU tables."""
from qiime.rarefaction import RarefactionMaker, get_rare_data, remove_empty_otus
from cogent.util.unit_test import TestCase, main
import numpy
class FunctionTests(TestCase):
def setUp(self):
self.otu_table_transpose = numpy.array([
[2,0,0,1],
[1,5,3,2],
[0,0,0,0],
])
self.otu_table = self.otu_table_transpose.T
self.sample_names = list('YXZ')
self.taxon_names = list('bacd')
self.otu_tuple = (self.sample_names, self.taxon_names,
self.otu_table_transpose.T, None)
def test_rarefy_to_list(self):
"""rarefy_to_list should rarefy correctly, same names, rm empty samples
"""
maker = RarefactionMaker(self.otu_tuple, 0, 1, 1, 1)
res = maker.rarefy_to_list(include_full=True)
self.assertFloatEqual(res[-1][2], self.sample_names)
self.assertFloatEqual(res[-1][3], self.taxon_names)
self.assertFloatEqual(res[-1][4], self.otu_table_transpose.T)
# each sample should have 1 seq, sample z should be removed
self.assertFloatEqual((res[1][4]).sum(0),[1.0,1.0] )
def test_get_empty_rare(self):
"""get_rare_data should be empty when depth > # seqs in any sample"""
rare_sample_ids, rare_otu_table = get_rare_data(
self.sample_names, self.otu_table, \
50, include_small_samples=False)
self.assertEqual(len(rare_sample_ids), 0)
self.assertEqual(rare_otu_table.size, 0)
def test_get_overfull_rare(self):
"""get_rare_data should be identical to given in this case
here, rare depth > any sample, and include_small... = True"""
rare_sample_ids, rare_otu_table = get_rare_data(
self.sample_names, self.otu_table, \
50, include_small_samples=True)
self.assertEqual(len(rare_sample_ids), 3)
self.assertEqual(rare_otu_table.size, 12)
for i, sam in enumerate(self.sample_names):
for j, otu in enumerate(self.taxon_names):
rare_val = rare_otu_table[self.taxon_names.index(otu),
rare_sample_ids.index(sam)]
self.assertEqual(rare_val, self.otu_table[j,i])
def test_get_11depth_rare(self):
"""get_rare_data should get only sample X
"""
rare_sample_ids, rare_otu_table = get_rare_data(
self.sample_names, self.otu_table, \
11, include_small_samples=False)
self.assertEqual(rare_sample_ids, ['X'])
#rare_otu_table[numpy.argsort(rare_otu_ids)]
self.assertEqual(rare_otu_table[numpy.argsort(self.taxon_names)][:,0],
numpy.array([5,1,3,2]))
def test_remove_empty_otus(self):
""" remove otus should match expected"""
otu_mtx = numpy.array([ [0,3,0,0],
[0,0,0,0],
[.1,0,0,0]])
otu_names = list('abc')
otu_lineages = ['lin1','lin2','lin3']
res_mtx, res_otu_names, res_lineages = \
remove_empty_otus(otu_mtx, otu_names, otu_lineages)
self.assertFloatEqual(res_mtx, numpy.array([[0,3,0,0],
[.1,0,0,0]]))
self.assertEqual(res_otu_names, list('ac'))
self.assertEqual(res_lineages, ['lin1','lin3'])
#run tests if called from command line
if __name__ == '__main__':
main()
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