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test_summarize_taxa.py
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test_summarize_taxa.py
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#!/usr/bin/env python
"""Tests of code for adding taxa to OTU table"""
__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project"
#remember to add yourself if you make changes
__credits__ = ["Rob Knight", "Daniel McDonald", "Antonio Gonzalez Pena", "Jose Carlos Clemente Litran"]
__license__ = "GPL"
__version__ = "1.5.0"
__maintainer__ = "Daniel McDonald"
__email__ = "wasade@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from qiime.summarize_taxa import make_summary, \
add_summary_mapping, sum_counts_by_consensus
from qiime.parse import parse_mapping_file
from qiime.util import convert_otu_table_relative
from numpy import array
from biom.table import table_factory
from biom.parse import parse_biom_table
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
self.otu_table_vals = array([[1,0,2,4],
[1,2,0,1],
[0,1,1,0],
[1,2,1,0]])
{(0, 0):1.0, (0, 2):2.0, (0, 3):4.0,
(1, 0):1.0, (1, 1):2.0, (1, 3):1.0,
(2, 1):1.0, (2, 2):1.0, (3, 0):1.0,
(3, 1): 2.0, (3, 2):1.0}
self.otu_table = table_factory(self.otu_table_vals,
['s1', 's2', 's3', 's4'],
['0', '1', '2', '3'],
None,
[{"taxonomy": ["Root", "Bacteria", "Actinobacteria", "Actinobacteria", "Coriobacteridae", "Coriobacteriales", "Coriobacterineae", "Coriobacteriaceae"]},
{"taxonomy": ["Root", "Bacteria", "Firmicutes", "\"Clostridia\""]},
{"taxonomy": ["Root", "Bacteria", "Firmicutes", "\"Clostridia\""]},
{"taxonomy": ["Root", "Bacteria"]}])
# self.otu_table="""#Full OTU Counts
##OTU ID\ts1\ts2\ts3\ts4\tConsensus Lineage
#0\t1\t0\t2\t4\tRoot;Bacteria;Actinobacteria;Actinobacteria;Coriobacteridae;Coriobacteriales;Coriobacterineae;Coriobacteriaceae
#1\t1\t2\t0\t1\tRoot;Bacteria;Firmicutes;"Clostridia"
#2\t0\t1\t1\t0\tRoot;Bacteria;Firmicutes;"Clostridia"
#3\t1\t2\t1\t0\tRoot;Bacteria""".split('\n')
self.mapping="""#SampleID\tBarcodeSequence\tTreatment\tDescription
#Test mapping file
s1\tAAAA\tControl\tControl mouse, I.D. 354
s2\tGGGG\tControl\tControl mouse, I.D. 355
s3\tCCCC\tExp\tDisease mouse, I.D. 356
s4\tTTTT\tExp\tDisease mouse, I.D. 357""".split('\n')
def test_sum_counts_by_consensus(self):
"""should sum otu counts by consensus"""
#otu_table = parse_otu_table(self.otu_table)
#otu_table = parse_biom_table(self.otu_table)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 3)
exp_result = {('Root','Bacteria','Actinobacteria'):array([1,0,2,4]),
('Root','Bacteria','Firmicutes'):array([1,3,1,1]),
('Root','Bacteria','Other'):array([1,2,1,0])}
exp_mapping = {'s1':0, 's2':1, 's3':2, 's4':3}
self.assertEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 2)
exp_result = {('Root','Bacteria'):array([3,5,4,5])}
exp_mapping = {'s1':0, 's2':1, 's3':2, 's4':3}
self.assertEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 4)
exp_result = {('Root','Bacteria','Actinobacteria','Actinobacteria'):\
array([1,0,2,4]),
('Root','Bacteria','Firmicutes','"Clostridia"'):\
array([1,3,1,1]),
('Root','Bacteria','Other','Other'):array([1,2,1,0])}
exp_mapping = {'s1':0, 's2':1, 's3':2, 's4':3}
self.assertEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
def test_make_new_summary_file(self):
"""make_new_summary_file works
"""
lower_percentage, upper_percentage = None, None
#otu_table = parse_otu_table(self.otu_table, int)
#otu_table = parse_biom_table(self.otu_table)
summary, header = make_summary(self.otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(header, ['Taxon','s1','s2','s3','s4'])
self.assertEqual(summary, [[('Root','Bacteria','Actinobacteria'),1,0,2,4],
[('Root','Bacteria','Firmicutes'),1,3,1,1],
[('Root','Bacteria','Other'),1,2,1,0]])
#test that works with relative abundances
#otu_table = parse_otu_table(self.otu_table, float)
#otu_table = parse_biom_table(self.otu_table, float)
#otu_table = convert_otu_table_relative(otu_table)
otu_table = self.otu_table.normObservationBySample()
summary, header = make_summary(otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(header, ['Taxon','s1','s2','s3','s4'])
self.assertEqual(summary[0][0], ('Root','Bacteria','Actinobacteria'))
self.assertFloatEqual(summary[0][1:], [1.0 / 3, 0.0, 0.5, 0.8])
self.assertEqual(summary[1][0], ('Root','Bacteria','Firmicutes'))
self.assertFloatEqual(summary[1][1:], [1.0 / 3, 0.6, 0.25, 0.2])
self.assertEqual(summary[2][0], ('Root','Bacteria','Other'))
self.assertFloatEqual(summary[2][1:], [1.0 / 3, 0.4, 0.25, 0.0])
##
# testing lower triming
lower_percentage, upper_percentage = 0.3, None
summary, header = make_summary(otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(summary[0][0], ('Root','Bacteria','Other'))
self.assertFloatEqual(summary[0][1:], [1.0 / 3, 0.4, 0.25, 0.0])
##
# testing upper triming
lower_percentage, upper_percentage = None, 0.4
summary, header = make_summary(otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(summary[0][0], ('Root','Bacteria','Actinobacteria'))
self.assertFloatEqual(summary[0][1:], [1.0 / 3, 0.0, 0.5, 0.8])
def test_add_summary_category_mapping(self):
"""make_new_summary_file works
"""
#otu_table = parse_otu_table(self.otu_table, int)
#otu_table = parse_biom_table(self.otu_table)
mapping, header, comments = parse_mapping_file(self.mapping)
summary, taxon_order = add_summary_mapping(self.otu_table, mapping, 3)
self.assertEqual(taxon_order, [('Root','Bacteria','Actinobacteria'),
('Root','Bacteria','Firmicutes'),
('Root','Bacteria','Other')])
self.assertEqual(summary, {'s1':[1,1,1],
's2':[0,3,2],
's3':[2,1,1],
's4':[4,1,0]})
#run unit tests if run from command-line
if __name__ == '__main__':
main()