def test_make_new_otu_counts(self):
"""make_new_otu_counts works
"""
mapping_lines = """#SampleID\tindividual\ttimepoint_zero\ttimepoint
AT0\tA\t1\t0
AT1\tA\t0\t1
AT2\tA\t0\t2
BT0\tB\t1\t0
BT1\tB\t0\t1
BT2\tB\t0\t2
""".split('\n')
mapping_data, header, comments = parse_mapping_file(mapping_lines)
samples_from_subject, sample_to_subtract = \
get_sample_individual_info(mapping_data, header, 'individual', \
'timepoint_zero')
otu_lines = """# QIIME v1.2.0-dev OTU table
#OTU ID\tAT0\tAT1\tS1\tAT2\tBT0\tBT1\tBT2
0\t0.5\t0.3\t99\t0.2\t0.0\t0.0\t0.0
1\t0.0\t0.0\t99\t0.0\t0.4\t0.5\t0.6
2\t0.1\t0.4\t99\t0.7\t0.5\t0.6\t0.8
3\t0.0\t0.1\t99\t0.0\t0.4\t0.0\t0.0
""".split('\n')
otu_table = parse_otu_table(otu_lines, float)
sample_ids, otu_ids, otu_counts, consensus = otu_table
converted_otu_table = make_new_otu_counts(otu_ids, sample_ids, otu_counts, consensus, sample_to_subtract, samples_from_subject)
converted_otu_table = converted_otu_table.split('\n')
self.assertEqual(converted_otu_table[1], "#OTU ID\tAT0\tAT1\tAT2\tBT0\tBT1\tBT2")
self.assertEqual(converted_otu_table[2], "0\t0.0\t-0.2\t-0.3\t999999999.0\t999999999.0\t999999999.0")
self.assertEqual(converted_otu_table[3], "1\t999999999.0\t999999999.0\t999999999.0\t0.0\t0.1\t0.2")
self.assertEqual(converted_otu_table[4], "2\t0.0\t0.3\t0.6\t0.0\t0.1\t0.3")
self.assertEqual(converted_otu_table[5], "3\t0.0\t0.1\t0.0\t0.0\t-0.4\t-0.4")
def test_make_new_otu_counts(self):
"""make_new_otu_counts works
"""
mapping_lines = """#SampleID\tindividual\ttimepoint_zero\ttimepoint
AT0\tA\t1\t0
AT1\tA\t0\t1
AT2\tA\t0\t2
BT0\tB\t1\t0
BT1\tB\t0\t1
BT2\tB\t0\t2
""".split('\n')
mapping_data, header, comments = parse_mapping_file(mapping_lines)
samples_from_subject, sample_to_subtract = \
get_sample_individual_info(mapping_data, header, 'individual',
'timepoint_zero')
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, 0.5], [0, 1, 0.29999999999999999], [0, 2, 99.0],
[0, 3, 0.20000000000000001], [1, 2, 99.0], [1, 4, 0.40000000000000002],
[1, 5, 0.5], [1, 6, 0.59999999999999998], [2, 0, 0.10000000000000001],
[2, 1, 0.40000000000000002], [2, 2, 99.0], [2, 3, 0.69999999999999996],
[2, 4, 0.5], [2, 5, 0.59999999999999998], [2, 6, 0.80000000000000004],
[3, 1, 0.10000000000000001], [3, 2, 99.0],
[3, 4, 0.40000000000000002]], "columns": [{"id": "AT0", "metadata":
null}, {"id": "AT1", "metadata": null}, {"id": "S1", "metadata": null},
{"id": "AT2", "metadata": null}, {"id": "BT0", "metadata": null},
{"id": "BT1", "metadata": null}, {"id": "BT2", "metadata": null}],
"generated_by": "QIIME 1.4.0-dev, svn revision 2570", "matrix_type":
"sparse", "shape": [4, 7], "format_url":
"http://www.qiime.org/svn_documentation/documentation/biom_format.html",
"date": "2011-12-21T21:35:19.499263", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
otu_table = parse_biom_table_str(otu_table_str)
converted_otu_table_object = make_new_otu_counts(otu_table,
sample_to_subtract, samples_from_subject)
expected_otu_table_str = """{"rows": [{"id": "0", "metadata": null},
{"id": "1", "metadata": null}, {"id": "2", "metadata": null}, {"id":
"3", "metadata": null}], "format":
"Biological Observation Matrix 0.9.0-dev", "data": [[0, 1,
-0.20000000000000001], [0, 2, -0.29999999999999999],
[0, 3, 999999999.0], [0, 4, 999999999.0], [0, 5, 999999999.0], [1, 0,
999999999.0], [1, 1, 999999999.0], [1, 2, 999999999.0], [1, 4,
0.10000000000000001], [1, 5, 0.20000000000000001], [2, 1,
0.29999999999999999], [2, 2, 0.59999999999999998], [2, 4,
0.10000000000000001], [2, 5, 0.29999999999999999], [3, 1,
0.10000000000000001], [3, 4, -0.40000000000000002], [3, 5,
-0.40000000000000002]], "columns": [{"id": "AT0", "metadata": null},
{"id": "AT1", "metadata": null}, {"id": "AT2", "metadata": null},
{"id": "BT0", "metadata": null}, {"id": "BT1", "metadata": null},
{"id": "BT2", "metadata": null}], "generated_by":
"QIIME 1.4.0-dev, svn revision 2570", "matrix_type": "sparse",
"shape": [4, 6], "format_url":
"http://biom-format.org",
"date": "2011-12-21T21:43:06.809380", "type": "OTU table", "id": null,
"matrix_element_type": "float"}"""
expected_otu_table_object = parse_biom_table_str(
expected_otu_table_str)
self.assertEqual(converted_otu_table_object.ObservationIds,
expected_otu_table_object.ObservationIds)
self.assertEqual(converted_otu_table_object.SampleIds,
expected_otu_table_object.SampleIds)
self.assertEqual(converted_otu_table_object.SampleMetadata,
expected_otu_table_object.SampleMetadata)
self.assertEqual(converted_otu_table_object.ObservationMetadata,
expected_otu_table_object.ObservationMetadata)
self.assertFloatEqual(sorted(converted_otu_table_object._data.items()),
sorted(expected_otu_table_object._data.items()))
