def test_output_results_G_test(self):
"""output_results works"""
category_info = {"sample1": "A", "sample2": "A", "sample3": "B", "sample4": "C"}
OTU_sample_info = {
"0": {"sample1": "0", "sample2": "0", "sample3": "1", "sample4": "1"},
"1": {"sample1": "1", "sample2": "1", "sample3": "1", "sample4": "0"},
"2": {"sample1": "0", "sample2": "0", "sample3": "1", "sample4": "1"},
"3": {"sample1": "0", "sample2": "1", "sample3": "0", "sample4": "1"},
}
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_sample_info, 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",
"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]",
"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]",
"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",
"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",
"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",
"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_output_results_G_test(self):
"""output_results works"""
category_info = {
'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'
}
OTU_sample_info = {
'0': {
'sample1': '0',
'sample2': '0',
'sample3': '1',
'sample4': '1'
},
'1': {
'sample1': '1',
'sample2': '1',
'sample3': '1',
'sample4': '0'
},
'2': {
'sample1': '0',
'sample2': '0',
'sample3': '1',
'sample4': '1'
},
'3': {
'sample1': '0',
'sample2': '1',
'sample3': '0',
'sample4': '1'
}
}
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_sample_info, 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',
'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]',
'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]',
'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',
'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',
'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',
'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_G_test_OTUs(self):
"""run_G_test_OTUs works"""
category_info = {
'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'
}
OTU_sample_info = {
'0': {
'sample1': '0',
'sample2': '0',
'sample3': '1',
'sample4': '1'
},
'1': {
'sample1': '1',
'sample2': '1',
'sample3': '0',
'sample4': '0'
},
'2': {
'sample1': '0',
'sample2': '0',
'sample3': '1',
'sample4': '0'
},
'3': {
'sample1': '0',
'sample2': '0',
'sample3': '0',
'sample4': '1'
}
}
category_values = ['A', 'B', 'C']
result = run_G_test_OTUs(['0', '1', '3'], category_info, \
OTU_sample_info, 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_sample_info = {
"0": {"sample1": "0", "sample2": "0", "sample3": "1", "sample4": "1"},
"1": {"sample1": "1", "sample2": "1", "sample3": "1", "sample4": "0"},
"2": {"sample1": "0", "sample2": "0", "sample3": "1", "sample4": "1"},
"3": {"sample1": "0", "sample2": "1", "sample3": "0", "sample4": "1"},
}
category_values = ["A", "B", "C"]
G_test_results = run_G_test_OTUs(["0", "1", "3"], category_info, OTU_sample_info, 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_fdr_correction_G_test(self):
"""fdr_correction_G_test works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
OTU_sample_info = {'0': {'sample1': '0', 'sample2': '0', 'sample3': '1', 'sample4': '1'},
'1': {'sample1': '1', 'sample2': '1', 'sample3': '1', 'sample4': '0'},
'2': {'sample1': '0', 'sample2': '0', 'sample3': '1', 'sample4': '1'},
'3': {'sample1': '0', 'sample2': '1', 'sample3': '0', 'sample4': '1'}}
category_values = ['A', 'B', 'C']
G_test_results = run_G_test_OTUs(['0', '1', '3'], category_info, \
OTU_sample_info, 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_run_G_test_OTUs(self):
"""run_G_test_OTUs works"""
category_info = {'sample1': 'A',
'sample2': 'A',
'sample3': 'B',
'sample4': 'C'}
OTU_sample_info = {'0': {'sample1': '0', 'sample2': '0', 'sample3': '1', 'sample4': '1'},
'1': {'sample1': '1', 'sample2': '1', 'sample3': '0', 'sample4': '0'},
'2': {'sample1': '0', 'sample2': '0', 'sample3': '1', 'sample4': '0'},
'3': {'sample1': '0', 'sample2': '0', 'sample3': '0', 'sample4': '1'}}
category_values = ['A', 'B', 'C']
result = run_G_test_OTUs(['0', '1', '3'], category_info, \
OTU_sample_info, 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_sample_info = {
'0': {
'sample1': '0',
'sample2': '0',
'sample3': '1',
'sample4': '1'
},
'1': {
'sample1': '1',
'sample2': '1',
'sample3': '1',
'sample4': '0'
},
'2': {
'sample1': '0',
'sample2': '0',
'sample3': '1',
'sample4': '1'
},
'3': {
'sample1': '0',
'sample2': '1',
'sample3': '0',
'sample4': '1'
}
}
category_values = ['A', 'B', 'C']
G_test_results = run_G_test_OTUs(['0', '1', '3'], category_info, \
OTU_sample_info, 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_sample_info = {'0': {'sample1': '0', 'sample2': '0', 'sample3': '1', 'sample4': '1'},
'1': {'sample1': '1', 'sample2': '1', 'sample3': '1', 'sample4': '0'},
'2': {'sample1': '0', 'sample2': '0', 'sample3': '1', 'sample4': '1'},
'3': {'sample1': '0', 'sample2': '1', 'sample3': '0', 'sample4': '1'}}
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_sample_info, 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', '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]', '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]', '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', '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', '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', '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_G_test_OTUs(self):
"""run_G_test_OTUs works"""
category_info = {"sample1": "A", "sample2": "A", "sample3": "B", "sample4": "C"}
OTU_sample_info = {
"0": {"sample1": "0", "sample2": "0", "sample3": "1", "sample4": "1"},
"1": {"sample1": "1", "sample2": "1", "sample3": "0", "sample4": "0"},
"2": {"sample1": "0", "sample2": "0", "sample3": "1", "sample4": "0"},
"3": {"sample1": "0", "sample2": "0", "sample3": "0", "sample4": "1"},
}
category_values = ["A", "B", "C"]
result = run_G_test_OTUs(["0", "1", "3"], category_info, OTU_sample_info, 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]},
},
)
