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#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2011-2017, 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.
# -----------------------------------------------------------------------------
import tempfile
from unittest import TestCase, main
import biom
from biom.cli.metadata_adder import _add_metadata
class TestAddMetadata(TestCase):
def setUp(self):
"""Set up data for use in unit tests."""
self.cmd = _add_metadata
with tempfile.NamedTemporaryFile('w') as fh:
fh.write(biom1)
fh.flush()
self.biom_table1 = biom.load_table(fh.name)
self.sample_md_lines1 = sample_md1.split('\n')
self.obs_md_lines1 = obs_md1.split('\n')
def test_add_sample_metadata_no_casting(self):
"""Correctly adds sample metadata without casting it."""
# Add a subset of sample metadata to a table that doesn't have any
# sample metadata to begin with. Don't perform any casting.
obs = self.cmd(table=self.biom_table1,
sample_metadata=self.sample_md_lines1)
self.assertEqual(obs.metadata()[obs.index('f4', 'sample')],
{'bar': '0.23', 'foo': '9', 'baz': 'abc;123'})
self.assertEqual(obs.metadata()[obs.index('not16S.1', 'sample')],
{'bar': '-4.2', 'foo': '0', 'baz': '123;abc'})
self.assertEqual(obs.metadata()[obs.index('f2', 'sample')], {})
def test_add_sample_metadata_with_casting(self):
"""Correctly adds sample metadata with casting."""
obs = self.cmd(table=self.biom_table1,
sample_metadata=self.sample_md_lines1,
sc_separated=['baz'], int_fields=['foo'],
float_fields=['bar'])
self.assertEqual(obs.metadata()[obs.index('f4', 'sample')],
{'bar': 0.23, 'foo': 9, 'baz': ['abc', '123']})
self.assertEqual(obs.metadata()[obs.index('not16S.1', 'sample')],
{'bar': -4.2, 'foo': 0, 'baz': ['123', 'abc']})
self.assertEqual(obs.metadata()[obs.index('f2', 'sample')], {})
def test_add_observation_metadata_no_casting(self):
"""Correctly adds observation metadata without casting it."""
# Add observation metadata to a table that already has observation
# metadata. Some observations won't be modified, and metadata for
# observations that aren't in the table are included. Don't perform any
# casting.
obs = self.cmd(table=self.biom_table1,
observation_metadata=self.obs_md_lines1)
metadata = obs.metadata(axis='observation')
self.assertEqual(
metadata[obs.index('None7', 'observation')],
{'foo': '6', 'taxonomy': 'abc;123|def;456'})
self.assertEqual(
metadata[obs.index('879972', 'observation')],
{'foo': '3', 'taxonomy': '123;abc|456;def'})
self.assertEqual(
metadata[obs.index('None8', 'observation')],
{'taxonomy': ['k__Bacteria']})
def test_add_observation_metadata_with_casting(self):
"""Correctly adds observation metadata with casting."""
obs = self.cmd(table=self.biom_table1,
observation_metadata=self.obs_md_lines1,
sc_pipe_separated=['taxonomy'], int_fields=['foo'])
metadata = obs.metadata(axis='observation')
self.assertEqual(
metadata[obs.index('None7', 'observation')],
{'foo': 6, 'taxonomy': [['abc', '123'], ['def', '456']]})
self.assertEqual(
metadata[obs.index('879972', 'observation')],
{'foo': 3, 'taxonomy': [['123', 'abc'], ['456', 'def']]})
self.assertEqual(
metadata[obs.index('None8', 'observation')],
{'taxonomy': ['k__Bacteria']})
biom1 = ('{"id": "None","format": "Biological Observation Matrix 1.0.0","form'
'at_url": "http://biom-format.org","type": "OTU table","generated_by'
'": "QIIME 1.6.0-dev","date": "2013-02-09T09:30:11.550590","matrix_t'
'ype": "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"]}},{"i'
'd": "42684", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobac'
'teria"]}},{"id": "None11", "metadata": {"taxonomy": ["Unclassified"'
']}},{"id": "None10", "metadata": {"taxonomy": ["Unclassified"]}},{"'
'id": "None7", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "N'
'one6", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None5", '
'"metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None4", "metadat'
'a": {"taxonomy": ["Unclassified"]}},{"id": "None3", "metadata": {"t'
'axonomy": ["k__Bacteria"]}},{"id": "None2", "metadata": {"taxonomy"'
': ["k__Bacteria"]}},{"id": "None1", "metadata": {"taxonomy": ["Uncl'
'assified"]}},{"id": "879972", "metadata": {"taxonomy": ["k__Bacteri'
'a"]}},{"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}]}')
sample_md1 = """#SampleID\tfoo\tbar\tbaz
f4\t9\t0.23\tabc;123
not16S.1\t0\t-4.2\t123;abc
"""
obs_md1 = """#OTUID\tfoo\ttaxonomy
None7\t6\tabc;123|def;456
best-observation\t8\tghi;789|jkl;101112
879972\t3\t123;abc|456;def
"""
if __name__ == "__main__":
main()
|
