def test_output_results_ANOVA(self):
"""output_results_ANOVA works"""
category_info = {"sample1": "A", "sample2": "A", "sample3": "B", "sample4": "B"}
OTU_sample_info = {
"0": {"sample1": "5", "sample2": "10", "sample3": "2", "sample4": "1"},
"1": {"sample1": "1", "sample2": "0", "sample3": "0", "sample4": "2"},
"2": {"sample1": "2", "sample2": "1", "sample3": "10", "sample4": "15"},
"3": {"sample1": "1", "sample2": "1.5", "sample3": "1.4", "sample4": "1.3"},
"4": {"sample1": "20", "sample2": "16", "sample3": "1.4", "sample4": "1.3"},
}
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_sample_info, 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",
"1\t0.698488655422\t3.49244327711\t0.873110819278\t0.5\t1.0\ttaxon2",
"0\t0.142857142857\t0.714285714286\t0.238095238095\t7.5\t1.5\ttaxon1",
"3\t0.732738758088\t3.66369379044\t0.732738758088\t1.25\t1.35\ttaxon4",
"2\t0.0497447318605\t0.248723659303\t0.124361829651\t1.5\t12.5\ttaxon3",
"4\t0.0141325222337\t0.0706626111683\t0.0706626111683\t18.0\t1.35\ttaxon5",
],
)
def test_output_results_ANOVA(self):
"""output_results_ANOVA works"""
category_info = {
'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'B'
}
OTU_sample_info = {
'0': {
'sample1': '5',
'sample2': '10',
'sample3': '2',
'sample4': '1'
},
'1': {
'sample1': '1',
'sample2': '0',
'sample3': '0',
'sample4': '2'
},
'2': {
'sample1': '2',
'sample2': '1',
'sample3': '10',
'sample4': '15'
},
'3': {
'sample1': '1',
'sample2': '1.5',
'sample3': '1.4',
'sample4': '1.3'
},
'4': {
'sample1': '20',
'sample2': '16',
'sample3': '1.4',
'sample4': '1.3'
}
}
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_sample_info, 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',
'1\t0.698488655422\t3.49244327711\t0.873110819278\t0.5\t1.0\ttaxon2',
'0\t0.142857142857\t0.714285714286\t0.238095238095\t7.5\t1.5\ttaxon1',
'3\t0.732738758088\t3.66369379044\t0.732738758088\t1.25\t1.35\ttaxon4',
'2\t0.0497447318605\t0.248723659303\t0.124361829651\t1.5\t12.5\ttaxon3',
'4\t0.0141325222337\t0.0706626111683\t0.0706626111683\t18.0\t1.35\ttaxon5'
])
def test_run_ANOVA_OTUs(self):
"""run_ANOVA_OTUs works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'B'}
OTU_sample_info = {'0': {'sample1': '5', 'sample2': '10', 'sample3': '2', 'sample4': '1'},
'1': {'sample1': '1', 'sample2': '0', 'sample3': '0', 'sample4': '2'},
'2': {'sample1': '2', 'sample2': '1', 'sample3': '10', 'sample4': '15'},
'3': {'sample1': '1', 'sample2': '1.5', 'sample3': '1.4', 'sample4': '1.3'}}
category_values = ['A', 'B']
result = run_ANOVA_OTUs(['0', '1', '3'], category_info,\
OTU_sample_info, 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_run_ANOVA_OTUs(self):
"""run_ANOVA_OTUs works"""
category_info = {
'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'B'
}
OTU_sample_info = {
'0': {
'sample1': '5',
'sample2': '10',
'sample3': '2',
'sample4': '1'
},
'1': {
'sample1': '1',
'sample2': '0',
'sample3': '0',
'sample4': '2'
},
'2': {
'sample1': '2',
'sample2': '1',
'sample3': '10',
'sample4': '15'
},
'3': {
'sample1': '1',
'sample2': '1.5',
'sample3': '1.4',
'sample4': '1.3'
}
}
category_values = ['A', 'B']
result = run_ANOVA_OTUs(['0', '1', '3'], category_info,\
OTU_sample_info, 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_run_ANOVA_OTUs(self):
"""run_ANOVA_OTUs works"""
category_info = {"sample1": "A", "sample2": "A", "sample3": "B", "sample4": "B"}
OTU_sample_info = {
"0": {"sample1": "5", "sample2": "10", "sample3": "2", "sample4": "1"},
"1": {"sample1": "1", "sample2": "0", "sample3": "0", "sample4": "2"},
"2": {"sample1": "2", "sample2": "1", "sample3": "10", "sample4": "15"},
"3": {"sample1": "1", "sample2": "1.5", "sample3": "1.4", "sample4": "1.3"},
}
category_values = ["A", "B"]
result = run_ANOVA_OTUs(["0", "1", "3"], category_info, OTU_sample_info, 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_sample_info = {'0': {'sample1': '5', 'sample2': '10', 'sample3': '2', 'sample4': '1'},
'1': {'sample1': '1', 'sample2': '0', 'sample3': '0', 'sample4': '2'},
'2': {'sample1': '2', 'sample2': '1', 'sample3': '10', 'sample4': '15'},
'3': {'sample1': '1', 'sample2': '1.5', 'sample3': '1.4', 'sample4': '1.3'},
'4': {'sample1': '20', 'sample2': '16', 'sample3': '1.4', 'sample4': '1.3'}}
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_sample_info, 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', '1\t0.698488655422\t3.49244327711\t0.873110819278\t0.5\t1.0\ttaxon2', '0\t0.142857142857\t0.714285714286\t0.238095238095\t7.5\t1.5\ttaxon1', '3\t0.732738758088\t3.66369379044\t0.732738758088\t1.25\t1.35\ttaxon4', '2\t0.0497447318605\t0.248723659303\t0.124361829651\t1.5\t12.5\ttaxon3', '4\t0.0141325222337\t0.0706626111683\t0.0706626111683\t18.0\t1.35\ttaxon5'])
