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#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2011-2015, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
from biom.cli.table_summarizer import _summarize_table
from biom.parse import load_table
import tempfile
from unittest import TestCase, main
class TestSummarizeTable(TestCase):
def setUp(self):
with tempfile.NamedTemporaryFile(mode='w') as fh:
fh.write(biom1)
fh.flush()
self.biom1 = load_table(fh.name)
def test_default(self):
""" TableSummarizer functions as expected
"""
result = _summarize_table(self.biom1)
# test same alphanumeric content, order of samples is runtime
# dependent
self.assertEqual(sorted(result), sorted(summary_default))
def test_qualitative(self):
""" TableSummarizer functions as expected with qualitative=True
"""
result = _summarize_table(self.biom1, qualitative=True)
# test same alphanumeric content, order of samples is runtime
# dependent
self.assertEqual(sorted(result), sorted(summary_qualitative))
biom1 = ('{"id": "None","format": "Biological Observation Matrix 1.0.0",'
'"format_url": "http://biom-format.org","type": "OTU table",'
'"generated_by": "QIIME 1.6.0-dev","date": '
'"2013-02-09T09:30:11.550590","matrix_type": "sparse",'
'"matrix_element_type": "int","shape": [14, 9],"data": [[0,0,20],'
'[0,1,18],[0,2,18],[0,3,22],[0,4,4],[1,4,1],[2,0,1],[2,4,1],[2,5,1],'
'[3,6,1],[4,4,1],[5,7,20],[6,4,1],[7,4,1],[7,5,1],[8,4,1],[8,6,2],'
'[8,8,3],[9,7,2],[10,5,1],[11,4,9],[11,5,20],[11,6,1],[11,8,4],'
'[12,4,3],[12,6,19],[12,8,15],[13,0,1],[13,1,4],[13,2,4]],"rows": '
'[{"id": "295053", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": '
'"42684", "metadata": {"taxonomy": ["k__Bacteria", '
'"p__Proteobacteria"]}},{"id": "None11", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "None10", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "None7", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "None6", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "None5", "metadata": {"taxonomy": '
'["k__Bacteria"]}},{"id": "None4", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "None3", "metadata": {"taxonomy": '
'["k__Bacteria"]}},{"id": "None2", "metadata": {"taxonomy": '
'["k__Bacteria"]}},{"id": "None1", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "879972", "metadata": {"taxonomy": '
'["k__Bacteria"]}},{"id": "None9", "metadata": {"taxonomy": '
'["Unclassified"]}},{"id": "None8", "metadata": {"taxonomy": '
'["k__Bacteria"]}}],"columns": [{"id": "f2", "metadata": null},'
'{"id": "f1", "metadata": null},{"id": "f3", "metadata": null},'
'{"id": "f4", "metadata": null},{"id": "p2", "metadata": null},{"id":'
' "p1", "metadata": null},{"id": "t1", "metadata": null},{"id": '
'"not16S.1", "metadata": null},{"id": "t2", "metadata": null}]}')
summary_default = """Num samples: 9
Num observations: 14
Total count: 200
Table density (fraction of non-zero values): 0.238
Counts/sample summary:
Min: 22.0
Max: 23.0
Median: 22.000
Mean: 22.222
Std. dev.: 0.416
Sample Metadata Categories: None provided
Observation Metadata Categories: taxonomy
Counts/sample detail:
p2: 22.0
f1: 22.0
f2: 22.0
f3: 22.0
f4: 22.0
t2: 22.0
not16S.1: 22.0
t1: 23.0
p1: 23.0"""
summary_qualitative = """Num samples: 9
Num observations: 14
Observations/sample summary:
Min: 1
Max: 9
Median: 3.000
Mean: 3.333
Std. dev.: 2.211
Sample Metadata Categories: None provided
Observation Metadata Categories: taxonomy
Observations/sample detail:
f4: 1
f1: 2
f3: 2
not16S.1: 2
f2: 3
t2: 3
t1: 4
p1: 4
p2: 9"""
if __name__ == "__main__":
main()
|
