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test_otu_category_significance.py
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test_otu_category_significance.py
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#!/usr/bin/env python
"""Tests of code for performing significance tests of OTU/category associations
"""
__author__ = "Catherine Lozupone"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Catherine Lozupone", "Dan Knights", "Jai Rideout"]
__license__ = "GPL"
__version__ = "1.5.0"
__maintainer__ = "Catherine Lozupone"
__email__ = "lozupone@colorado.edu"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from qiime.otu_category_significance import filter_OTUs, \
make_contingency_matrix, run_single_G_test, run_G_test_OTUs, \
add_fdr_correction_to_results, output_results_G_test, \
run_single_ANOVA, run_ANOVA_OTUs, output_results_ANOVA,\
run_correlation_OTUs, run_single_correlation, output_results_correlation,\
get_taxonomy_info, get_category_info,\
aggregate_multiple_results_ANOVA, aggregate_multiple_results_G_test,\
aggregate_multiple_results_correlation, get_common_OTUs,\
test_wrapper_multiple, test_wrapper, get_single_correlation_values,\
run_paired_T_test_OTUs, run_single_paired_T_test, \
get_single_paired_T_values, output_results_paired_T_test, sort_rows
from numpy import array
from cogent.util.dict2d import Dict2D
from qiime.util import get_tmp_filename
from os import remove
from qiime.parse import parse_mapping_file
from biom.parse import parse_biom_table_str
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def test_filter_OTUs(self):
"""filter_OTUs works"""
otu_table_str = """{"rows": [{"id": "0", "metadata": {}}, {"id": "1",
"metadata": {}}, {"id": "2", "metadata": {}}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 1, 2.0],
[1, 0, 1.0], [2, 0, 1.0], [2, 1, 1.0], [2, 2, 1.0]], "columns":
[{"id": "sample1", "metadata": null},
{"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2541",
"matrix_type": "sparse", "shape": [3, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T10:13:37.373053", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
taxonomy_info = get_taxonomy_info(otu_table)
result = filter_OTUs(otu_table, 2)
self.assertEqual(result, [])
result = filter_OTUs(otu_table, 1)
self.assertEqual(result, ['0', '1'])
result = filter_OTUs(otu_table, 2, False)
self.assertEqual(result, ['2'])
result = filter_OTUs(otu_table, 1, False)
self.assertEqual(result, ['0', '1', '2'])
#test that is works if a category mapping file is supplied
cat_mapping = {'sample2': '0', 'sample3': '1'}
result = filter_OTUs(otu_table, 1, category_mapping_info=cat_mapping)
self.assertEqual(result, ['0'])
#test that works with a max filter
result = filter_OTUs(otu_table, 1, False, max_filter=2)
self.assertEqual(result, ['0', '1'])
def test_make_contingency_matrix(self):
"""make_contingency_matrix works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id":
"1", "metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 2, 1.0], [0, 3, 1.0], [1, 0, 1.0], [1, 1, 1.0],
[2, 2, 1.0], [3, 3, 1.0]], "columns": [{"id": "sample1", "metadata":
null}, {"id": "sample2", "metadata": null}, {"id": "sample3",
"metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:29:40.964867", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B', 'C']
result = make_contingency_matrix('0', category_info, otu_table,
category_values)
self.assertEqual(result['OTU_pos']['B_pos'], 1)
self.assertEqual(result['OTU_pos']['C_pos'], 1)
self.assertEqual(result['OTU_pos']['A_pos'], 0)
self.assertEqual(result['OTU_neg']['A_pos'], 2)
self.assertEqual(result['OTU_neg']['B_pos'], 0)
self.assertEqual(result['OTU_neg']['C_pos'], 0)
def test_run_single_G_test(self):
"""run_single_G_test works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id":
"1", "metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 2, 1.0], [0, 3, 1.0], [1, 0, 1.0], [1, 1, 1.0],
[2, 2, 1.0], [3, 3, 1.0]], "columns": [{"id": "sample1", "metadata":
null}, {"id": "sample2", "metadata": null}, {"id": "sample3",
"metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:29:40.964867", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B', 'C']
g_val, prob, contingency_matrix = run_single_G_test('0', category_info,
otu_table, category_values)
self.assertFloatEqual(g_val, 4.29304060218)
self.assertFloatEqual(prob, 0.508041627088)
self.assertEqual(contingency_matrix, {'OTU_pos': {'B_pos': [1, 0.5], 'C_pos': [1, 0.5], 'A_pos': [0, 1.0]}, 'OTU_neg': {'B_pos': [0, 0.5], 'C_pos': [0, 0.5], 'A_pos': [2, 1.0]}})
#check that it works if samples in mapping are not in OTU table
otu_table2_str = """{"rows": [{"id": "0", "metadata": null}, {"id":
"1", "metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 1, 1.0], [0, 2, 1.0], [1, 0, 1.0], [2, 1, 1.0],
[3, 2, 1.0]], "columns": [{"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}, {"id": "sample4", "metadata":
null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2570",
"matrix_type": "sparse", "shape": [4, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:36:52.105159", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table2 = parse_biom_table_str(otu_table2_str)
g_val, prob, contingency_matrix = run_single_G_test('0', category_info,
otu_table2, category_values)
self.assertFloatEqual(contingency_matrix, {'OTU_pos': {'B_pos': [1, 0.66666666666666663], 'C_pos': [1, 0.66666666666666663], 'A_pos': [0, 0.66666666666666663]}, 'OTU_neg': {'B_pos': [0, 0.33333333333333331], 'C_pos': [0, 0.33333333333333331], 'A_pos': [1, 0.33333333333333331]}})
#check that it works is samples in the OTU table are not in the mapping
category_info2 = {'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
g_val, prob, contingency_matrix = run_single_G_test('0',
category_info2, otu_table, category_values)
self.assertFloatEqual(contingency_matrix, {'OTU_pos': {'B_pos': [1, 0.66666666666666663], 'C_pos': [1, 0.66666666666666663], 'A_pos': [0, 0.66666666666666663]}, 'OTU_neg': {'B_pos': [0, 0.33333333333333331], 'C_pos': [0, 0.33333333333333331], 'A_pos': [1, 0.33333333333333331]}})
def test_run_single_ANOVA(self):
"""run_single_ANOVA works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'B'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 0, 5.0], [0, 1, 10.0], [0, 2, 2.0], [0, 3, 1.0],
[1, 0, 0.0015], [1, 1, 0.0015], [2, 0, 2.0], [2, 2, 1.0], [3, 3, 1.0]],
"columns": [{"id": "sample1", "metadata": null}, {"id": "sample2",
"metadata": null}, {"id": "sample3", "metadata": null},
{"id": "sample4", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2570", "matrix_type": "sparse",
"shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:47:04.545731", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B']
group_means, prob = run_single_ANOVA('0', category_info, otu_table,
category_values)
self.assertEqual(group_means, [7.5, 1.5])
self.assertFloatEqual(prob, 0.142857142857)
#test that it works when there are samples in the cat mapping
#that are not in the OTU table
otu_table2_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 10.0],
[0, 1, 2.0], [0, 2, 1.0], [1, 0, 1.0], [2, 1, 1.0], [3, 2, 1.0]],
"columns": [{"id": "sample2", "metadata": null}, {"id": "sample3",
"metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:49:34.052074", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table2 = parse_biom_table_str(otu_table2_str)
group_means, prob = run_single_ANOVA('0', category_info,\
otu_table2, category_values)
self.assertEqual(group_means, [10.0, 1.5])
#test that it works when there are samples that are in the OTU
#table that are not in the category mapping
category_info2 = {'sample2': 'A',
'sample3': 'B',
'sample4': 'B'}
group_means, prob = run_single_ANOVA('0', category_info2,\
otu_table, category_values)
self.assertEqual(group_means, [10.0, 1.5])
def test_run_single_correlation(self):
"""run_single_correlation works"""
category_info = {'sample1': '1',
'sample2': '2',
'sample3': '3',
'sample4': '4'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 0, 1.0], [0, 1, 2.0], [0, 2, 2.0], [0, 3, 4.0],
[1, 0, 1.0], [1, 1, 2.0], [1, 2, 3.0], [1, 3, 4.0], [2, 0, 4.0],
[2, 1, 3.0], [2, 2, 2.0], [2, 3, 1.0], [3, 0, 1.0], [3, 1, 2.0],
[3, 2, 3.0], [3, 3, 5.0]], "columns": [{"id": "sample1", "metadata":
null}, {"id": "sample2", "metadata": null}, {"id": "sample3",
"metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:52:44.318249", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B']
otu_ab_vals, cat_vals = get_single_correlation_values('0', category_info,\
otu_table)
r, prob = run_single_correlation(otu_ab_vals, cat_vals, filter=1)
self.assertFloatEqual(r, 0.923380516877)
self.assertFloatEqual(prob, 0.0766194831234)
def test_get_single_correlation_values(self):
"""get_single_correlation_values works
"""
category_info = {'sample1': '1',
'sample2': '2',
'sample3': '3',
'sample4': '4'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 0, 1.0], [0, 1, 2.0], [0, 2, 2.0], [0, 3, 4.0],
[1, 0, 1.0], [1, 1, 2.0], [1, 2, 3.0], [1, 3, 4.0], [2, 0, 4.0],
[2, 1, 3.0], [2, 2, 2.0], [2, 3, 1.0], [3, 0, 1.0], [3, 1, 2.0],
[3, 2, 3.0], [3, 3, 5.0]], "columns": [{"id": "sample1", "metadata":
null}, {"id": "sample2", "metadata": null}, {"id": "sample3",
"metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:52:44.318249", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B']
OTU_abundance_values, category_values = get_single_correlation_values(\
'0', category_info, otu_table)
self.assertEqual(OTU_abundance_values, [4.0, 1.0, 2.0, 2.0])
self.assertEqual(category_values, [4.0, 1.0, 3.0, 2.0])
#works if the otu table is missing samples
otu_table2_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null}, {"id":
"3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 2.0],
[0, 1, 2.0], [0, 2, 4.0], [1, 0, 2.0], [1, 1, 3.0], [1, 2, 4.0],
[2, 0, 3.0], [2, 1, 2.0], [2, 2, 1.0], [3, 0, 2.0], [3, 1, 3.0],
[3, 2, 5.0]], "columns": [{"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}, {"id": "sample4", "metadata":
null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2570",
"matrix_type": "sparse", "shape": [4, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:56:21.469203", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table2 = parse_biom_table_str(otu_table2_str)
OTU_abundance_values, category_values = get_single_correlation_values(\
'0', category_info, otu_table2)
self.assertEqual(OTU_abundance_values, [4.0, 2.0, 2.0])
self.assertEqual(category_values, [4.0, 3.0, 2.0])
#works if the category mapping file is missing samples
category_info2 = {'sample2': '2',
'sample3': '3',
'sample4': '4'}
OTU_abundance_values, category_values = get_single_correlation_values(\
'0', category_info2, otu_table)
self.assertEqual(OTU_abundance_values, [4.0, 2.0, 2.0])
self.assertEqual(category_values, [4.0, 3.0, 2.0])
def test_get_single_correlation_values_ignore_val(self):
"""get_single_correlation_values works with ignore val"""
category_info = {'sample1': '1',
'sample2': '2',
'sample3': '3',
'sample4': '4'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 0, 99999.0], [0, 1, 2.0], [0, 2, 2.0], [0, 3, 4.0],
[1, 0, 1.0], [1, 1, 2.0], [1, 2, 3.0], [1, 3, 4.0], [2, 0, 4.0],
[2, 1, 3.0], [2, 2, 2.0], [2, 3, 1.0], [3, 0, 1.0], [3, 1, 2.0],
[3, 2, 3.0], [3, 3, 5.0]], "columns": [{"id": "sample1", "metadata":
null}, {"id": "sample2", "metadata": null}, {"id": "sample3",
"metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T19:15:22.356507", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
OTU_abundance_values, category_values = \
get_single_correlation_values('0', category_info, otu_table, \
ignore_val=99999.0)
self.assertEqual(OTU_abundance_values, [4.0, 2.0, 2.0])
self.assertEqual(category_values, [4.0, 3.0, 2.0])
def test_get_single_paired_T_values(self):
"""get_single_paired_T_values works"""
cat_mapping = """#SampleID\ttimepoint_zero\tindividual
s1\t1\tA
s2\t0\tA
s3\t1\tB
s4\t0\tB
s5\t1\tC
s6\t0\tC""".split('\n')
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id":
"1", "metadata": null}, {"id": "2", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 999999999.0],
[0, 1, 999999999.0], [0, 3, 0.29999999999999999],
[0, 5, 0.20000000000000001], [1, 1, -0.20000000000000001],
[1, 2, 999999999.0], [1, 3, 999999999.0], [1, 4, 999999999.0],
[1, 5, 999999999.0], [2, 1, 0.20000000000000001],
[2, 3, -0.69999999999999996], [2, 5, 0.10000000000000001]],
"columns": [{"id": "s1", "metadata": null},
{"id": "s2", "metadata": null}, {"id": "s3", "metadata": null},
{"id": "s4", "metadata": null}, {"id": "s5", "metadata": null},
{"id": "s6", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [3, 6], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:00:27.397644", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
mapping_data, header, comments = parse_mapping_file(cat_mapping)
taxonomy_info = get_taxonomy_info(otu_table)
OTU_list = ['0', '1', '2']
before_vals, after_vals = get_single_paired_T_values('0', \
mapping_data, header, 'individual', 'timepoint_zero', \
otu_table, 999999999.0)
self.assertFloatEqual(before_vals, [0.0, 0.0])
self.assertFloatEqual(after_vals, [0.3, 0.2])
#test of OTU1
before_vals, after_vals = get_single_paired_T_values('1',
mapping_data, header, 'individual', 'timepoint_zero',
otu_table, 999999999.0)
self.assertFloatEqual(before_vals, [0.0])
self.assertFloatEqual(after_vals, [-0.2])
#works when a sample is missing from the OTU table
#e.g. if an after timepoint dropped out during rarefaction
#will also drop the before
otu_table2_str = """{"rows": [{"id": "0", "metadata": null}, {"id":
"1", "metadata": null}, {"id": "2", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 999999999.0], [0,
1, 999999999.0], [0, 3, 0.29999999999999999], [1, 1,
-0.20000000000000001], [1, 2, 999999999.0], [1, 3, 999999999.0], [1, 4,
999999999.0], [2, 1, 0.20000000000000001], [2, 3,
-0.69999999999999996]], "columns": [{"id": "s1", "metadata": null},
{"id": "s2", "metadata": null}, {"id": "s3", "metadata": null}, {"id":
"s4", "metadata": null}, {"id": "s5", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2564", "matrix_type":
"sparse", "shape": [3, 5], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:13:14.199954", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table2 = parse_biom_table_str(otu_table2_str)
before_vals, after_vals = get_single_paired_T_values('0',
mapping_data, header, 'individual', 'timepoint_zero', otu_table2,
999999999.0)
self.assertEqual(before_vals, [0.0])
self.assertFloatEqual(after_vals, [0.3])
#works when the before is missing
otu_table3_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null}],
"format": "Biological Observation Matrix v0.9",
"data": [[0, 0, 999999999.0], [0, 1, 999999999.0],
[0, 3, 0.29999999999999999], [0, 4, 0.20000000000000001],
[1, 1, -0.20000000000000001], [1, 2, 999999999.0], [1, 3, 999999999.0],
[1, 4, 999999999.0], [2, 1, 0.20000000000000001],
[2, 3, -0.69999999999999996], [2, 4, 0.10000000000000001]], "columns":
[{"id": "s1", "metadata": null}, {"id": "s2", "metadata": null},
{"id": "s3", "metadata": null}, {"id": "s4", "metadata": null},
{"id": "s6", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [3, 5], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:14:52.851951", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table3 = parse_biom_table_str(otu_table3_str)
before_vals, after_vals = get_single_paired_T_values('0',
mapping_data, header, 'individual', 'timepoint_zero', otu_table3,
999999999.0)
self.assertEqual(before_vals, [0.0])
self.assertFloatEqual(after_vals, [0.3])
def test_run_single_paired_T_test(self):
"""run_single_paired_T_test works
"""
cat_mapping = """#SampleID\ttimepoint_zero\tindividual
s1\t1\tA
s2\t0\tA
s3\t1\tB
s4\t0\tB
s5\t1\tC
s6\t0\tC""".split('\n')
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 999999999.0],
[0, 1, 999999999.0], [0, 3, 0.29999999999999999],
[0, 5, 0.20000000000000001], [1, 1, -0.20000000000000001],
[1, 2, 999999999.0], [1, 3, 999999999.0], [1, 4, 999999999.0],
[1, 5, 999999999.0], [2, 1, 0.20000000000000001],
[2, 3, -0.69999999999999996], [2, 5, 0.10000000000000001]], "columns":
[{"id": "s1", "metadata": null}, {"id": "s2", "metadata": null},
{"id": "s3", "metadata": null}, {"id": "s4", "metadata": null}, {"id":
"s5", "metadata": null}, {"id": "s6", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [3, 6], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:17:58.541124", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
mapping_data, header, comments = parse_mapping_file(cat_mapping)
taxonomy_info = get_taxonomy_info(otu_table)
OTU_list = ['0', '1', '2']
#should return the results since there should be 4 values to evaluate
result = run_single_paired_T_test('0', mapping_data, header,
'individual', 'timepoint_zero', otu_table, 999999999.0, 4)
self.assertEqual(len(result), 4)
self.assertFloatEqual(result[1], 0.12566591637800242)
self.assertFloatEqual(result[2], [0.29999999999999999, 0.20000000000000001])
self.assertEqual(result[3], 2)
#check the the filter works
result = run_single_paired_T_test('0', mapping_data, header,
'individual', 'timepoint_zero', otu_table, 999999999.0, 5)
self.assertEqual(result, None)
def test_run_paired_T_test_OTUs(self):
"""run_single_paired_T_test works
"""
cat_mapping = """#SampleID\ttimepoint_zero\tindividual
s1\t1\tA
s2\t0\tA
s3\t1\tB
s4\t0\tB
s5\t1\tC
s6\t0\tC""".split('\n')
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 999999999.0],
[0, 1, 999999999.0], [0, 3, 0.29999999999999999],
[0, 5, 0.20000000000000001], [1, 1, -0.20000000000000001],
[1, 2, 999999999.0], [1, 3, 999999999.0], [1, 4, 999999999.0],
[1, 5, 999999999.0], [2, 1, 0.20000000000000001],
[2, 3, -0.69999999999999996], [2, 5, 0.10000000000000001]], "columns":
[{"id": "s1", "metadata": null}, {"id": "s2", "metadata": null},
{"id": "s3", "metadata": null}, {"id": "s4", "metadata": null},
{"id": "s5", "metadata": null}, {"id": "s6", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2564", "matrix_type":
"sparse", "shape": [3, 6], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:10:53.571949", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
mapping_data, header, comments = parse_mapping_file(cat_mapping)
taxonomy_info = get_taxonomy_info(otu_table)
OTU_list = ['0', '1', '2']
all_results = run_paired_T_test_OTUs(OTU_list, mapping_data, header, \
'individual', 'timepoint_zero', otu_table, 999999999.0, 4)
self.assertFloatEqual(all_results, {'0': [-4.9999999999999982, 0.12566591637800242, 0.25, 2], '2': [0.46816458878452216, 0.68573031947264562, -0.1333333333333333, 3]})
def test_output_results_paired_T_test(self):
"""output_results_paired_T_test works
"""
cat_mapping = """#SampleID\ttimepoint_zero\tindividual
s1\t1\tA
s2\t0\tA
s3\t1\tB
s4\t0\tB
s5\t1\tC
s6\t0\tC""".split('\n')
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 0, 999999999.0],
[0, 1, 999999999.0], [0, 3, 0.29999999999999999],
[0, 5, 0.20000000000000001], [1, 1, -0.20000000000000001],
[1, 2, 999999999.0], [1, 3, 999999999.0], [1, 4, 999999999.0],
[1, 5, 999999999.0], [2, 1, 0.20000000000000001],
[2, 3, -0.69999999999999996], [2, 5, 0.10000000000000001]], "columns":
[{"id": "s1", "metadata": null}, {"id": "s2", "metadata": null},
{"id": "s3", "metadata": null}, {"id": "s4", "metadata": null},
{"id": "s5", "metadata": null}, {"id": "s6", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2564", "matrix_type":
"sparse", "shape": [3, 6], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:06:21.731328", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
mapping_data, header, comments = parse_mapping_file(cat_mapping)
taxonomy_info = get_taxonomy_info(otu_table)
OTU_list = ['0', '1', '2']
all_results = run_paired_T_test_OTUs(OTU_list, mapping_data, header, \
'individual', 'timepoint_zero', otu_table, 999999999.0, 4)
output = output_results_paired_T_test(all_results)
self.assertEqual(output, ['OTU\tprob\tT stat\taverage_diff\tnum_pairs\tBonferroni_corrected\tFDR_corrected', '0\t0.125665916378\t-5.0\t0.25\t2\t0.251331832756\t0.251331832756', '2\t0.685730319473\t0.468164588785\t-0.133333333333\t3\t1.37146063895\t0.685730319473'])
def test_run_ANOVA_OTUs(self):
"""run_ANOVA_OTUs works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'B'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}, {"id": "3",
"metadata": null}], "format": "Biological Observation Matrix v0.9",
"data": [[0, 0, 5.0], [0, 1, 10.0], [0, 2, 2.0], [0, 3, 1.0],
[1, 0, 1.0], [1, 3, 2.0], [2, 0, 2.0], [2, 1, 1.0], [2, 2, 10.0],
[2, 3, 15.0], [3, 0, 1.0], [3, 1, 1.5], [3, 2, 1.3999999999999999],
[3, 3, 1.3]], "columns": [{"id": "sample1", "metadata": null},
{"id": "sample2", "metadata": null}, {"id": "sample3", "metadata":
null}, {"id": "sample4", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:03:44.355433", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B']
result = run_ANOVA_OTUs(['0', '1', '3'], category_info,\
otu_table, category_values)
self.assertEqual(result, {'1': [[0.5, 1.0], 0.69848865542223582, 2.0954659662667074], '0': [[7.5, 1.5], 0.14285714285714285, 0.42857142857142855], '3': [[1.25, 1.3500000000000001], 0.73273875808757438, 2.1982162742627231]})
def test_output_results_ANOVA(self):
"""output_results_ANOVA works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'B'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}, {"id": "4", "metadata": null}],
"format": "Biological Observation Matrix v0.9", "data": [[0, 0, 5.0],
[0, 1, 10.0], [0, 2, 2.0], [0, 3, 1.0], [1, 0, 1.0], [1, 3, 2.0],
[2, 0, 2.0], [2, 1, 1.0], [2, 2, 10.0], [2, 3, 15.0], [3, 0, 1.0],
[3, 1, 1.5], [3, 2, 1.3999999999999999], [3, 3, 1.3], [4, 0, 20.0],
[4, 1, 16.0], [4, 2, 1.3999999999999999], [4, 3, 1.3]], "columns":
[{"id": "sample1", "metadata": null}, {"id": "sample2", "metadata":
null}, {"id": "sample3", "metadata": null}, {"id": "sample4",
"metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [5, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T18:00:27.098306", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B']
taxonomy_info = {'0': 'taxon1',
'1': 'taxon2',
'2': 'taxon3',
'3': 'taxon4',
'4': 'taxon5'}
ANOVA_results = run_ANOVA_OTUs(['0', '2', '1', '3', '4'], category_info,\
otu_table, category_values)
output = output_results_ANOVA(ANOVA_results, category_values,\
taxonomy_info)
self.assertEqual(output, ['OTU\tprob\tBonferroni_corrected\tFDR_corrected\tA_mean\tB_mean\tConsensus Lineage', '4\t0.0141325222337\t0.0706626111683\t0.0706626111683\t18.0\t1.35\ttaxon5', '2\t0.0497447318605\t0.248723659303\t0.124361829651\t1.5\t12.5\ttaxon3', '0\t0.142857142857\t0.714285714286\t0.238095238095\t7.5\t1.5\ttaxon1', '1\t0.698488655422\t3.49244327711\t0.873110819278\t0.5\t1.0\ttaxon2', '3\t0.732738758088\t3.66369379044\t0.732738758088\t1.25\t1.35\ttaxon4'])
def test_run_G_test_OTUs(self):
"""run_G_test_OTUs works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 2, 1.0],
[0, 3, 1.0], [1, 0, 1.0], [1, 1, 1.0], [2, 2, 1.0], [3, 3, 1.0]],
"columns": [{"id": "sample1", "metadata": null}, {"id": "sample2",
"metadata": null}, {"id": "sample3", "metadata": null}, {"id":
"sample4", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:57:12.451685", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B', 'C']
result = run_G_test_OTUs(['0', '1', '3'], category_info, \
otu_table, category_values)
self.assertEqual(result.keys(), ['1', '0', '3'])
self.assertFloatEqual(result['0'][3], 1.5241248812628101)
self.assertFloatEqual(result['0'][0], 4.29304060218)
self.assertFloatEqual(result['0'][1], 0.508041627088)
self.assertEqual(result['0'][2], {'OTU_pos': {'B_pos': [1, 0.5], 'C_pos': [1, 0.5], 'A_pos': [0, 1.0]}, 'OTU_neg': {'B_pos': [0, 0.5], 'C_pos': [0, 0.5], 'A_pos': [2, 1.0]}})
def test_fdr_correction_G_test(self):
"""fdr_correction_G_test works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 2, 1.0],
[0, 3, 1.0], [1, 0, 1.0], [1, 1, 1.0], [1, 2, 1.0], [2, 2, 1.0],
[2, 3, 1.0], [3, 1, 1.0], [3, 3, 1.0]], "columns": [{"id": "sample1",
"metadata": null}, {"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}, {"id": "sample4", "metadata":
null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2564",
"matrix_type": "sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:52:54.285800", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B', 'C']
G_test_results = run_G_test_OTUs(['0', '1', '3'], category_info, \
otu_table, category_values)
G_test_results = add_fdr_correction_to_results(G_test_results)
self.assertFloatEqual(G_test_results['0'][-1], 1.52412488126)
self.assertFloatEqual(G_test_results['1'][-1], 0.938976340277)
self.assertFloatEqual(G_test_results['3'][-1], 0.828522198394)
def test_output_results_G_test(self):
"""output_results works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 2, 1.0],
[0, 3, 1.0], [1, 0, 1.0], [1, 1, 1.0], [1, 2, 1.0], [2, 2, 1.0],
[2, 3, 1.0], [3, 1, 1.0], [3, 3, 1.0]], "columns": [{"id": "sample1",
"metadata": null}, {"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}, {"id": "sample4", "metadata":
null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2564",
"matrix_type": "sparse", "shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:52:54.285800", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
category_values = ['A', 'B', 'C']
taxonomy_info = {'0': 'taxon1',
'1': 'taxon2',
'2': 'taxon3',
'3': 'taxon4'}
G_test_results = run_G_test_OTUs(['0', '1', '3'], category_info, \
otu_table, category_values)
output = output_results_G_test(G_test_results, {})
self.assertEqual(output, ['OTU\tg_val\tg_prob\tBonferroni_corrected\tFDR_corrected\tOTU_pos##B_pos\tOTU_pos##C_pos\tOTU_pos##A_pos\tOTU_neg##B_pos\tOTU_neg##C_pos\tOTU_neg##A_pos', '0\t4.29304060218\t0.508041627088\t1.52412488126\t1.52412488126\t[1, 0.5]\t[1, 0.5]\t[0, 1.0]\t[0, 0.5]\t[0, 0.5]\t[2, 1.0]', '1\t3.48284992796\t0.625984226851\t1.87795268055\t0.938976340277\t[1, 0.75]\t[0, 0.75]\t[2, 1.5]\t[0, 0.25]\t[1, 0.25]\t[0, 0.5]', '3\t2.14652030109\t0.828522198394\t2.48556659518\t0.828522198394\t[0, 0.5]\t[1, 0.5]\t[1, 1.0]\t[1, 0.5]\t[0, 0.5]\t[1, 1.0]'])
output = output_results_G_test(G_test_results, taxonomy_info)
self.assertEqual(output, ['OTU\tg_val\tg_prob\tBonferroni_corrected\tFDR_corrected\tOTU_pos##B_pos\tOTU_pos##C_pos\tOTU_pos##A_pos\tOTU_neg##B_pos\tOTU_neg##C_pos\tOTU_neg##A_pos\tConsensus Lineage', '0\t4.29304060218\t0.508041627088\t1.52412488126\t1.52412488126\t[1, 0.5]\t[1, 0.5]\t[0, 1.0]\t[0, 0.5]\t[0, 0.5]\t[2, 1.0]\ttaxon1', '1\t3.48284992796\t0.625984226851\t1.87795268055\t0.938976340277\t[1, 0.75]\t[0, 0.75]\t[2, 1.5]\t[0, 0.25]\t[1, 0.25]\t[0, 0.5]\ttaxon2', '3\t2.14652030109\t0.828522198394\t2.48556659518\t0.828522198394\t[0, 0.5]\t[1, 0.5]\t[1, 1.0]\t[1, 0.5]\t[0, 0.5]\t[1, 1.0]\ttaxon4'])
def test_run_correlation_OTUs(self):
"""run_correlation_OTUs works"""
category_info = {'sample1':'0.1',
'sample2':'0.2',
'sample3':'0.3',
'sample4':'0.4'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 1, 1.0],
[0, 2, 2.0], [0, 3, 3.0], [1, 0, 7.0], [1, 1, 5.0], [1, 2, 3.0],
[1, 3, 1.0], [2, 0, 4.0], [2, 1, 4.2000000000000002], [2, 2, 4.0],
[2, 3, 4.0], [3, 1, 1.0], [3, 3, 1.0]], "columns": [{"id": "sample1",
"metadata": null}, {"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}, {"id": "sample4",
"metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:44:54.905035", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
OTU_list = ['1', '0', '2', '3']
result = run_correlation_OTUs(OTU_list, category_info, otu_table)
#OTU 0 should be positively correlated, 1 negative, and 2&3 neutral
self.assertFloatEqual(result['0'][0], 1.0)#r
self.assertFloatEqual(result['0'][1], 0.0)#prob
self.assertEqual(result['0'][2], "[3.0, 0.0, 2.0, 1.0]")
x = result['0'][3]
x = x[1:-1]
x = x.split(',')
x = [float(i) for i in x]
self.assertFloatEqual(x, [0.40000000000000002, 0.10000000000000001, 0.29999999999999999, 0.20000000000000001])
self.assertFloatEqual(result['1'][0], -0.99999999999999956)
self.assertFloatEqual(result['1'][1], 4.4408920985006281e-16)
y = result['1'][2]
y = y[1:-1]
y = y.split(',')
y = [float(i) for i in y]
self.assertFloatEqual(y, [1.0, 7.0, 3.0, 5.0])
#test that appropriate error is raised is categorical
category_info = {'sample1':'A',
'sample2':'B',
'sample3':'A',
'sample4':'B'}
self.assertRaises(ValueError, run_correlation_OTUs, OTU_list,
category_info, otu_table)
def test_output_results_correlation(self):
"""output_results_correlation works"""
category_info = {'sample1':'0.1',
'sample2':'0.2',
'sample3':'0.3',
'sample4':'0.4'}
otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null},
{"id": "3", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 1, 1.0],
[0, 2, 2.0], [0, 3, 3.0], [1, 0, 7.0], [1, 1, 5.0], [1, 2, 3.0],
[1, 3, 1.0], [2, 0, 4.0], [2, 1, 4.2000000000000002], [2, 2, 4.0],
[2, 3, 4.0], [3, 1, 1.0], [3, 3, 1.0]], "columns": [{"id": "sample1",
"metadata": null}, {"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}, {"id": "sample4",
"metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [4, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:44:54.905035", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
taxonomy_info = {'0': 'taxon1',
'1': 'taxon2',
'2': 'taxon3',
'3': 'taxon4'}
OTU_list = ['1', '0', '2', '3']
result = run_correlation_OTUs(OTU_list, category_info, otu_table)
output = output_results_correlation(result, taxonomy_info)
self.assertEqual(output[0], 'OTU\tprob\totu_values_y\tcat_values_x\tBonferroni_corrected\tFDR_corrected\tr\tConsensus Lineage')
line2 = output[2].split('\t')
self.assertEqual(line2[0], '1')
self.assertFloatEqual(float(line2[1]), 4.4408920985e-16)
self.assertFloatEqual(float(line2[4]), 1.7763568394e-15)
self.assertFloatEqual(float(line2[5]), 8.881784197e-16)
self.assertFloatEqual(float(line2[6]), -1.0)
self.assertFloatEqual(line2[7], 'taxon2')
self.assertEqual(len(output), 5)
def test_get_taxonomy_info(self):
"""get_taxonomy_info works"""
otu_table_str = """{"rows": [{"id": "0", "metadata": null}, {"id": "1",
"metadata": null}, {"id": "2", "metadata": null}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 1, 2.0],
[1, 0, 1.0], [2, 0, 1.0], [2, 1, 1.0], [2, 2, 1.0]], "columns":
[{"id": "sample1", "metadata": null}, {"id": "sample2", "metadata":
null}, {"id": "sample3", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [3, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:27:12.329308", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
taxonomy_info = get_taxonomy_info(otu_table)
self.assertEqual(taxonomy_info, {})
#test that it parses otu tables with taxonomy fields appropriately
otu_table_str = """{"rows": [{"id": "0", "metadata": {"taxonomy":
["Bacteria", "Bacteroidetes", "Bacteroidales", "Parabacteroidaceae",
"Unclassified", "otu_475"]}}, {"id": "1", "metadata": {"taxonomy":
["Bacteria", "Bacteroidetes", "Bacteroidales", "adhufec77-25",
"Barnesiella", "Barnesiella_viscericola", "otu_369"]}}, {"id": "2",
"metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Clostridia",
"Clostridiales", "Faecalibacterium", "Unclassified", "otu_1121"]}}],
"format": "Biological Observation Matrix v0.9", "data": [[0, 1, 2.0],
[1, 0, 1.0], [2, 0, 1.0], [2, 1, 1.0], [2, 2, 1.0]], "columns":
[{"id": "sample1", "metadata": null}, {"id": "sample2", "metadata":
null}, {"id": "sample3", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [3, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:31:44.658057", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
taxonomy_info = get_taxonomy_info(otu_table)
self.assertEqual(taxonomy_info, {'1':
'Bacteria; Bacteroidetes; Bacteroidales; adhufec77-25; ' + \
'Barnesiella; Barnesiella_viscericola; otu_369', '0':
'Bacteria; Bacteroidetes; Bacteroidales; Parabacteroidaceae; ' + \
'Unclassified; otu_475', '2':
'Bacteria; Firmicutes; Clostridia; Clostridiales; ' + \
'Faecalibacterium; Unclassified; otu_1121'})
def test_get_category_info(self):
"""get_category_info works"""
category_mapping = """#SampleID\tcat1\tcat2
sample1\tA\t0
sample2\tB\t8.0
sample3\tC\t1.0""".split('\n')
mapping_data, header, comments = parse_mapping_file(category_mapping)
result, cat_vals = get_category_info(mapping_data, header, 'cat1')
self.assertEqual(result, {'sample1': 'A', 'sample3': 'C', 'sample2': 'B'})
self.assertEqual(cat_vals, (['A', 'B', 'C']))
mapping_data, header, comments = parse_mapping_file(category_mapping)
result, cat_vals = get_category_info(mapping_data, header, \
'cat2', threshold=5.0)
self.assertEqual(result, {'sample1': '0', 'sample3': '0', 'sample2': '1'})
self.assertEqual(cat_vals, (['0', '1']))
def test_test_wrapper(self):
"""runs the specified statistical test"""
otu_table1 = """{"rows": [{"id": "0", "metadata": {"taxonomy":
["lineage0"]}}, {"id": "1", "metadata": {"taxonomy": ["lineage1"]}},
{"id": "2", "metadata": {"taxonomy": ["lineage2"]}}],
"format": "Biological Observation Matrix v0.9", "data": [[0, 0, 1.0],
[0, 1, 2.0], [0, 3, 1.0], [1, 0, 1.0], [1, 3, 1.0], [2, 0, 1.0],
[2, 1, 1.0], [2, 2, 1.0], [2, 3, 1.0]], "columns": [{"id": "sample1",
"metadata": null}, {"id": "sample2", "metadata": null}, {"id":
"sample3", "metadata": null}, {"id": "sample4", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2556", "matrix_type":
"sparse", "shape": [3, 4], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T15:42:03.286885", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
category_mapping = ['#SampleID\tcat1\tcat2',
'sample1\tA\t0',
'sample2\tA\t8.0',
'sample3\tB\t1.0',
'sample4\tB\t1.0']
OTU_list = ['1', '0']
fp1 = get_tmp_filename()
try:
f1 = open(fp1,'w')
except IOError, e:
raise e,"Could not create temporary files: %s, %s" %(f1)
f1.write(otu_table1)
f1.close()
# ANOVA
otu_table_path = fp1
threshold = None
_filter = 0
otu_include = None
otu_table1 = open(fp1,'U')
category = 'cat1'
# get expected ANOVA output from file
results1 = test_wrapper('ANOVA', otu_table1, category_mapping, \
category, threshold, _filter, otu_include=None)
self.assertEqual(len(results1), 4)
self.assertEqual(results1[0], 'OTU\tprob\tBonferroni_corrected\tFDR_corrected\tA_mean\tB_mean\tConsensus Lineage')
otu0_results = results1[1].split('\t')
A_mean = float(otu0_results[4])
self.assertFloatEqual(A_mean, 0.5)
B_mean = float(otu0_results[5])
self.assertFloatEqual(B_mean, 0.166666666666666)
# get expected ANOVA means when it is specified not to convert the table to relative abundance
otu_table_path = fp1
otu_table1 = open(fp1,'U')
results1 = test_wrapper('ANOVA', otu_table1, category_mapping, \
category, threshold, _filter, otu_include=None, otu_table_relative_abundance=True)
self.assertEqual(len(results1), 4)
self.assertEqual(results1[0], 'OTU\tprob\tBonferroni_corrected\tFDR_corrected\tA_mean\tB_mean\tConsensus Lineage')
otu0_results = results1[1].split('\t')
A_mean = float(otu0_results[4])
self.assertFloatEqual(A_mean, 1.5)
B_mean = float(otu0_results[5])
self.assertFloatEqual(B_mean, 0.5)
# correlation
otu_table_paths = fp1
threshold = None
_filter = 0
otu_include = None
otu_table1 = open(fp1,'U')
results1 = test_wrapper('correlation', otu_table1, category_mapping, \
'cat2', threshold, _filter, otu_include=None)
self.assertEqual(len(results1), 4)
self.assertEqual(results1[0], 'OTU\tprob\totu_values_y\tcat_values_x\tBonferroni_corrected\tFDR_corrected\tr\tConsensus Lineage')
remove(fp1)
def test_aggregate_multiple_results_ANOVA(self):
"""aggregate_multiple_results_ANOVA works"""
all_results = {
'0':[[[10,20],.05,.1], [[12,18],.1,.2]],
'1':[[[15,14],.5,1], [[12,11],.6, 1.2]]
}
result = aggregate_multiple_results_ANOVA(all_results)
self.assertFloatEqual(result['0'], [array([11,19]),.075, .15])
self.assertFloatEqual(result['1'], [array([13.5,12.5]),.55, 1.1])
def test_aggregate_multiple_results_G_test(self):
"""aggregate_multiple_results_G_test works"""
cm_0_0 = Dict2D({'OTU_pos':{'A_pos':2, 'B_pos':0},
'OTU_neg':{'A_pos':3,'B_pos':4}},Default=0, Pad=True)
cm_0_1 = Dict2D({'OTU_pos':{'A_pos':5, 'B_pos':1},
'OTU_neg':{'A_pos':6,'B_pos':10}},Default=0, Pad=True)
cm_1_0 = Dict2D({'OTU_pos':{'A_pos':3, 'B_pos':5},
'OTU_neg':{'A_pos':1,'B_pos':1}},Default=0, Pad=True)
cm_1_1 = Dict2D({'OTU_pos':{'A_pos':4, 'B_pos':4},
'OTU_neg':{'A_pos':0,'B_pos':1}},Default=0, Pad=True)
exp_cm_0 = Dict2D({'OTU_pos':{'A_pos':3.5, 'B_pos':0.5},
'OTU_neg':{'A_pos':4.5,'B_pos':7}},Default=0, Pad=True)
exp_cm_1 = Dict2D({'OTU_pos':{'A_pos':3.5, 'B_pos':4.5},
'OTU_neg':{'A_pos':.5,'B_pos':1}},Default=0, Pad=True)
all_results = {\
'0':[[.5, .05, cm_0_0, .1], [.6,.1,cm_0_1,.2]],
'1':[[.6, .5, cm_1_0, 1], [.8,.6, cm_1_1, 1.2]]
}
results = aggregate_multiple_results_G_test(all_results)
self.assertFloatEqual(results['0'], [0.55, 0.075, exp_cm_0, .15])
self.assertFloatEqual(results['1'], [0.7, 0.55, exp_cm_1, 1.1])
def test_aggregate_multiple_results_correlation(self):
"""aggregate_multiple_results_correlation works"""
all_results = {
'0':[[-1,.05,'NA', 'NA',.1], [-.5,.1,'NA','NA',.2]],
'1':[[.4,.5,'NA','NA',1], [.5,.6,'NA','NA', 1.2]]
}
result = aggregate_multiple_results_correlation(all_results)
self.assertFloatEqual(result['0'], [-.75, .075, 'NA', 'NA'])
self.assertFloatEqual(result['1'], [.45,.55, 'NA', 'NA'])
def test_get_common_OTUs(self):
"""get_common_OTUs works"""
# create the temporary OTU tables
otu_table1 = """{"rows": [{"id": "0", "metadata": {"taxonomy":
["lineage0"]}}, {"id": "1", "metadata": {"taxonomy": ["lineage1"]}},
{"id": "2", "metadata": {"taxonomy": ["lineage2"]}}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 1, 2.0],
[1, 0, 1.0], [2, 0, 1.0], [2, 1, 1.0], [2, 2, 1.0]], "columns":
[{"id": "sample1", "metadata": null}, {"id": "sample2", "metadata":
null}, {"id": "sample3", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [3, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T17:19:22.290776", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table2 = """{"rows": [{"id": "0", "metadata": {"taxonomy":
["lineage0"]}}, {"id": "1", "metadata": {"taxonomy": ["lineage1"]}},
{"id": "2", "metadata": {"taxonomy": ["lineage2"]}}], "format":
"Biological Observation Matrix v0.9", "data": [[0, 1, 2.0],
[1, 0, 1.0], [2, 1, 1.0], [2, 2, 1.0]], "columns": [{"id": "sample1",
"metadata": null}, {"id": "sample2", "metadata": null},
{"id": "sample3", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2564", "matrix_type": "sparse",
"shape": [3, 3], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",