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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.
# -----------------------------------------------------------------------------
from os.path import abspath, dirname, join
import tempfile
import numpy as np
from biom.cli.table_converter import _convert
from biom.parse import MetadataMap
from biom.table import Table
from biom import load_table
from biom.parse import biom_open, parse_biom_table
from unittest import TestCase, main
class TableConverterTests(TestCase):
def setUp(self):
"""Set up data for use in unit tests."""
self.cmd = _convert
self.output_filepath = tempfile.NamedTemporaryFile().name
with tempfile.NamedTemporaryFile('w') as fh:
fh.write(biom1)
fh.flush()
self.biom_table1 = load_table(fh.name)
self.biom_lines1 = biom1.split('\n')
with tempfile.NamedTemporaryFile('w') as fh:
fh.write(classic1)
fh.flush()
self.classic_biom1 = load_table(fh.name)
self.sample_md1 = MetadataMap.from_file(sample_md1.split('\n'))
test_data_dir = join(dirname(abspath(__file__)), 'test_data')
self.json_collapsed_obs = join(test_data_dir,
'json_obs_collapsed.biom')
self.json_collapsed_samples = join(test_data_dir,
'json_sample_collapsed.biom')
def test_classic_to_biom(self):
"""Correctly converts classic to biom."""
self.cmd(table=self.classic_biom1,
output_filepath=self.output_filepath,
to_json=True, table_type='OTU table')
obs = load_table(self.output_filepath)
self.assertEqual(type(obs), Table)
self.assertEqual(len(obs.ids()), 9)
self.assertEqual(len(obs.ids(axis='observation')), 14)
self.assertEqual(obs.metadata(), None)
self.assertNotEqual(obs.metadata(axis='observation'), None)
def test_classic_to_biom_with_metadata(self):
"""Correctly converts classic to biom with metadata."""
# No processing of metadata.
obs = self.cmd(table=self.classic_biom1,
output_filepath=self.output_filepath,
sample_metadata=self.sample_md1, to_json=True,
table_type='OTU table', process_obs_metadata='naive')
obs = load_table(self.output_filepath)
self.assertEqual(type(obs), Table)
self.assertEqual(len(obs.ids()), 9)
self.assertEqual(len(obs.ids(axis='observation')), 14)
self.assertNotEqual(obs.metadata(), None)
self.assertNotEqual(obs.metadata(axis='observation'), None)
self.assertEqual(obs.metadata()[obs.index(u'p2', u'sample')],
{'foo': 'c;b;a'})
self.assertEqual(obs.metadata()[obs.index('not16S.1', 'sample')],
{'foo': 'b;c;d'})
self.assertEqual(obs.metadata(axis='observation')[
obs.index('None11', 'observation')],
{'taxonomy': 'Unclassified'})
# With processing of metadata (currently only supports observation md).
obs = self.cmd(table=self.classic_biom1,
output_filepath=self.output_filepath,
sample_metadata=self.sample_md1, table_type='OTU table',
process_obs_metadata='sc_separated', to_json=True)
obs = load_table(self.output_filepath)
self.assertEqual(type(obs), Table)
self.assertEqual(len(obs.ids()), 9)
self.assertEqual(len(obs.ids(axis='observation')), 14)
self.assertNotEqual(obs.metadata(), None)
self.assertNotEqual(obs.metadata(axis='observation'), None)
self.assertEqual(obs.metadata()[obs.index('p2', 'sample')],
{'foo': 'c;b;a'})
self.assertEqual(obs.metadata()[obs.index('not16S.1', 'sample')],
{'foo': 'b;c;d'})
self.assertEqual(obs.metadata(axis='observation')[
obs.index('None11', 'observation')],
{'taxonomy': ['Unclassified']})
def test_biom_to_classic1(self):
"""Correctly converts biom to classic."""
self.cmd(table=self.biom_table1,
output_filepath=self.output_filepath,
to_tsv=True, header_key='taxonomy')
self.assertEqual(load_table(self.output_filepath), self.classic_biom1)
def test_biom_to_classic2(self):
"""Correctly converts biom to classic with metadata renaming."""
self.cmd(table=self.biom_table1,
output_filepath=self.output_filepath, to_tsv=True,
header_key='taxonomy', output_metadata_id='foo')
obs = load_table(self.output_filepath)
self.assertTrue('foo' in obs.metadata(axis='observation')[0])
def test_json_to_hdf5_collapsed_samples(self):
"""Correctly converts json to HDF5 changing the sample metadata"""
with biom_open(self.json_collapsed_samples) as f:
obs = self.cmd(table=parse_biom_table(f),
output_filepath=self.output_filepath, to_hdf5=True,
collapsed_samples=True)
obs = load_table(self.output_filepath)
exp = Table(np.array([[0., 1.], [6., 6.], [6., 1.],
[1., 4.], [0., 2.]]),
observation_ids=[u'GG_OTU_1', u'GG_OTU_2', u'GG_OTU_3',
u'GG_OTU_4', u'GG_OTU_5'],
sample_ids=[u'skin', u'gut'],
observation_metadata=[
{u'taxonomy': [u'k__Bacteria', u'p__Proteobacteria',
u'c__Gammaproteobacteria',
u'o__Enterobacteriales',
u'f__Enterobacteriaceae',
u'g__Escherichia', u's__']},
{u'taxonomy': [u'k__Bacteria', u'p__Cyanobacteria',
u'c__Nostocophycideae',
u'o__Nostocales', u'f__Nostocaceae',
u'g__Dolichospermum', u's__']},
{u'taxonomy': [u'k__Archaea', u'p__Euryarchaeota',
u'c__Methanomicrobia',
u'o__Methanosarcinales',
u'f__Methanosarcinaceae',
u'g__Methanosarcina', u's__']},
{u'taxonomy': [u'k__Bacteria', u'p__Firmicutes',
u'c__Clostridia', u'o__Halanaerobiales',
u'f__Halanaerobiaceae',
u'g__Halanaerobium',
u's__Halanaerobiumsaccharolyticum']},
{u'taxonomy': [u'k__Bacteria', u'p__Proteobacteria',
u'c__Gammaproteobacteria',
u'o__Enterobacteriales',
u'f__Enterobacteriaceae',
u'g__Escherichia', u's__']}],
sample_metadata=[
{u'collapsed_ids': [u'Sample4', u'Sample5',
u'Sample6']},
{u'collapsed_ids': [u'Sample1', u'Sample2',
u'Sample3']}
],
type=u'OTU table')
self.assertEqual(obs, exp)
def test_json_to_hdf5_collapsed_metadata(self):
"""Correctly converts json to HDF5 changing the observation metadata"""
with biom_open(self.json_collapsed_obs) as f:
t = parse_biom_table(f)
obs = self.cmd(table=t,
output_filepath=self.output_filepath, to_hdf5=True,
collapsed_observations=True)
obs = load_table(self.output_filepath)
exp = Table(np.array([[2., 1., 1., 0., 0., 1.],
[0., 0., 1., 4., 0., 2.],
[5., 1., 0., 2., 3., 1.],
[0., 1., 2., 0., 0., 0.]]),
observation_ids=[u'p__Firmicutes', u'p__Euryarchaeota',
u'p__Cyanobacteria',
u'p__Proteobacteria'],
sample_ids=[u'Sample1', u'Sample2', u'Sample3',
u'Sample4', u'Sample5', u'Sample6'],
observation_metadata=[
{u'collapsed_ids': [u'GG_OTU_4']},
{u'collapsed_ids': [u'GG_OTU_3']},
{u'collapsed_ids': [u'GG_OTU_2']},
{u'collapsed_ids': [u'GG_OTU_1', u'GG_OTU_5']}],
sample_metadata=[
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CGCTTATCGAGA',
u'Description': u'human gut',
u'BODY_SITE': u'gut'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CATACCAGTAGC',
u'Description': u'human gut',
u'BODY_SITE': u'gut'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCTACCTGT',
u'Description': u'human gut',
u'BODY_SITE': u'gut'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCGGCCTGT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCTACCAAT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTAACTACCAAT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'}],
type=u'OTU table')
self.assertEqual(obs, exp)
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": "float",
"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}]
}"""
classic1 = """# Constructed from biom file
#OTU ID\tf2\tf1\tf3\tf4\tp2\tp1\tt1\tnot16S.1\tt2\ttaxonomy
295053\t20.0\t18.0\t18.0\t22.0\t4.0\t0.0\t0.0\t0.0\t0.0\tk__Bacteria
42684\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\tk__Bacteria; """ + \
"""p__Proteobacteria
None11\t1.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t0.0\tUnclassified
None10\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\tUnclassified
None7\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\tUnclassified
None6\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t20.0\t0.0\tUnclassified
None5\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\tk__Bacteria
None4\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t0.0\tUnclassified
None3\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t2.0\t0.0\t3.0\tk__Bacteria
None2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t2.0\t0.0\tk__Bacteria
None1\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\tUnclassified
879972\t0.0\t0.0\t0.0\t0.0\t9.0\t20.0\t1.0\t0.0\t4.0\tk__Bacteria
None9\t0.0\t0.0\t0.0\t0.0\t3.0\t0.0\t19.0\t0.0\t15.0\tUnclassified
None8\t1.0\t4.0\t4.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\tk__Bacteria"""
sample_md1 = """#SampleID\tfoo
f4\ta;b;c
not16S.1\tb;c;d
f2\ta;c;d
f1\ta;b;c
p2\tc;b;a
f3\ta;b;c
t1\tt;b;c
p1\tp;b;c
t2\tt;2;z
"""
if __name__ == "__main__":
main()
|
