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test_humann.py
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test_humann.py
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# ----------------------------------------------------------------------------
# Copyright (c) 2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import pandas as pd
from qiime2.plugin.testing import TestPluginBase
from q2_sapienns import HumannGeneFamilyFormat, HumannPathAbundanceFormat
from q2_sapienns._humann import humann_genefamily, humann_pathway
class HumannTests(TestPluginBase):
package = 'q2_sapienns.tests'
class HumannGeneFamilyTests(HumannTests):
def test_humann_genefamilies(self):
_, input_table_df = self.transform_format(
HumannGeneFamilyFormat, pd.DataFrame, 'humann-genefamilies-1.tsv'
)
obs_table, obs_tax = humann_genefamily(input_table_df)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (1, 8))
self.assertEqual(list(obs_table.index), ['sample1'])
self.assertEqual(
list(obs_table.columns),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris']) # noqa: E501
self.assertEqual(list(obs_table.T['sample1']),
[150.0, 57.0, 5.0, 4.0,
1.0, 31.0, 22.0, 7.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (8, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris']) # noqa: E501
self.assertEqual(
list(obs_tax['Taxon']),
['UniRef50_unknown; g__Bacteroides; s__Bacteroides_fragilis',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_stercoris']) # noqa: E501
def test_humann_genefamilies_unchanged_sample_ids(self):
_, input_table_df = self.transform_format(
HumannGeneFamilyFormat, pd.DataFrame, 'humann-genefamilies-1.tsv'
)
obs_table, obs_tax = humann_genefamily(
input_table_df, strip_units_from_sample_ids=False)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (1, 8))
self.assertEqual(list(obs_table.index), ['sample1_Abundance-RPKs'])
self.assertEqual(
list(obs_table.columns),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris']) # noqa: E501
self.assertEqual(list(obs_table.T['sample1_Abundance-RPKs']),
[150.0, 57.0, 5.0, 4.0,
1.0, 31.0, 22.0, 7.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (8, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris']) # noqa: E501
self.assertEqual(
list(obs_tax['Taxon']),
['UniRef50_unknown; g__Bacteroides; s__Bacteroides_fragilis',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_stercoris']) # noqa: E501
def test_humann_genefamilies_multi_sample(self):
_, input_table_df = self.transform_format(
HumannGeneFamilyFormat, pd.DataFrame, 'humann-genefamilies-2.tsv'
)
obs_table, obs_tax = humann_genefamily(input_table_df)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (2, 10))
self.assertEqual(list(obs_table.index), ['sample1', 'sample_2'])
self.assertEqual(
list(obs_table.columns),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_unknown|g__Bacteroides.s__Bacteroides_finegoldii',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|unclassified'])
self.assertEqual(list(obs_table.T['sample1']),
[150.0, 25.0, 57.0, 5.0, 4.0,
1.0, 31.0, 22.0, 7.0, 0.0])
self.assertEqual(list(obs_table.T['sample_2']),
[0.0, 25.0, 0.0, 0.0, 0.0, 0.0,
40.0, 2.0, 2.0, 1.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (10, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_unknown|g__Bacteroides.s__Bacteroides_finegoldii',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|unclassified'])
self.assertEqual(
list(obs_tax['Taxon']),
['UniRef50_unknown; g__Bacteroides; s__Bacteroides_fragilis',
'UniRef50_unknown; g__Bacteroides; s__Bacteroides_finegoldii',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_stercoris', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; unclassified'])
def test_humann_genefamilies_multi_sample_unchanged_sample_ids(self):
_, input_table_df = self.transform_format(
HumannGeneFamilyFormat, pd.DataFrame, 'humann-genefamilies-2.tsv'
)
obs_table, obs_tax = humann_genefamily(
input_table_df, strip_units_from_sample_ids=False
)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (2, 10))
self.assertEqual(list(obs_table.index),
['sample1_Abundance-RPKs', 'sample_2_Abundance-RPKs'])
self.assertEqual(
list(obs_table.columns),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_unknown|g__Bacteroides.s__Bacteroides_finegoldii',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|unclassified'])
self.assertEqual(list(obs_table.T['sample1_Abundance-RPKs']),
[150.0, 25.0, 57.0, 5.0, 4.0,
1.0, 31.0, 22.0, 7.0, 0.0])
self.assertEqual(list(obs_table.T['sample_2_Abundance-RPKs']),
[0.0, 25.0, 0.0, 0.0, 0.0, 0.0,
40.0, 2.0, 2.0, 1.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (10, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UniRef50_unknown|g__Bacteroides.s__Bacteroides_fragilis',
'UniRef50_unknown|g__Bacteroides.s__Bacteroides_finegoldii',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon|unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|g__Bacteroides.s__Bacteroides_stercoris', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase|unclassified'])
self.assertEqual(
list(obs_tax['Taxon']),
['UniRef50_unknown; g__Bacteroides; s__Bacteroides_fragilis',
'UniRef50_unknown; g__Bacteroides; s__Bacteroides_finegoldii',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_fragilis', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; g__Bacteroides; s__Bacteroides_stercoris', # noqa: E501
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon; unclassified', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_vulgatus', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_thetaiotaomicron', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; g__Bacteroides; s__Bacteroides_stercoris', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase; unclassified'])
def test_humann_genefamilies_multi_sample_destratify(self):
_, input_table_df = self.transform_format(
HumannGeneFamilyFormat, pd.DataFrame, 'humann-genefamilies-2.tsv'
)
obs_table, obs_tax = humann_genefamily(input_table_df, destratify=True)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (2, 4))
self.assertEqual(list(obs_table.index), ['sample1', 'sample_2'])
self.assertEqual(
list(obs_table.columns),
['UNMAPPED',
'UniRef50_unknown',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase'])
self.assertEqual(list(obs_table.T['sample1']),
[187.0, 150.0, 67.0, 60.0])
self.assertEqual(list(obs_table.T['sample_2']),
[42.0, 50.0, 0.0, 45.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (4, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UNMAPPED',
'UniRef50_unknown',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase'])
self.assertEqual(
list(obs_tax['Taxon']),
['UNMAPPED',
'UniRef50_unknown',
'UniRef50_A6L0N6: Conserved protein found in conjugate transposon', # noqa: E501
'UniRef50_O83668: Fructose-bisphosphate aldolase'])
class HumannPathwayTests(HumannTests):
def test_humann_pathway(self):
_, input_table_df = self.transform_format(
HumannPathAbundanceFormat, pd.DataFrame,
'humann-pathabundance-1.tsv'
)
obs_table, obs_tax = humann_pathway(input_table_df)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (1, 9))
self.assertEqual(list(obs_table.index), ['sample1'])
self.assertEqual(
list(obs_table.columns),
['UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae',
'UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii',
'UNINTEGRATED|unclassified',
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation|unclassified',
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|unclassified'])
self.assertEqual(list(obs_table.T['sample1']),
[23.0, 20.0, 12.0, 32.5, 4.5,
3.0, 16.7, 8.0, 6.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (9, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae',
'UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii',
'UNINTEGRATED|unclassified',
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation|unclassified',
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|unclassified'])
self.assertEqual(
list(obs_tax['Taxon']),
['UNINTEGRATED; g__Bacteroides; s__Bacteroides_caccae',
'UNINTEGRATED; g__Bacteroides; s__Bacteroides_finegoldii',
'UNINTEGRATED; unclassified',
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation; unclassified',
'PWY-5484: glycolysis II (from fructose-6P); g__Bacteroides; s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P); g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P); unclassified'])
def test_humann_pathway_unchanged_sample_ids(self):
_, input_table_df = self.transform_format(
HumannPathAbundanceFormat, pd.DataFrame,
'humann-pathabundance-1.tsv'
)
obs_table, obs_tax = humann_pathway(
input_table_df, strip_units_from_sample_ids=False)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (1, 9))
self.assertEqual(list(obs_table.index), ['sample1_Abundance'])
self.assertEqual(
list(obs_table.columns),
['UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae',
'UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii',
'UNINTEGRATED|unclassified',
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation|unclassified',
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|unclassified'])
self.assertEqual(list(obs_table.T['sample1_Abundance']),
[23.0, 20.0, 12.0, 32.5, 4.5,
3.0, 16.7, 8.0, 6.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (9, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae',
'UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii',
'UNINTEGRATED|unclassified',
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation|unclassified',
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|unclassified'])
self.assertEqual(
list(obs_tax['Taxon']),
['UNINTEGRATED; g__Bacteroides; s__Bacteroides_caccae',
'UNINTEGRATED; g__Bacteroides; s__Bacteroides_finegoldii',
'UNINTEGRATED; unclassified',
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation; unclassified',
'PWY-5484: glycolysis II (from fructose-6P); g__Bacteroides; s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P); g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P); unclassified'])
def test_humann_pathway_multisample(self):
_, input_table_df = self.transform_format(
HumannPathAbundanceFormat, pd.DataFrame,
'humann-pathabundance-2.tsv'
)
obs_table, obs_tax = humann_pathway(input_table_df)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (2, 10))
self.assertEqual(list(obs_table.index), ['sample1', 'sample_2'])
self.assertEqual(
list(obs_table.columns),
['UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae',
'UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii',
'UNINTEGRATED|unclassified',
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'PWY0-1301: melibiose degradation|unclassified',
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|unclassified'])
self.assertEqual(list(obs_table.T['sample1']),
[23.0, 20.0, 12.0, 32.5, 4.5,
0.0, 3.0, 16.7, 8.0, 6.0])
self.assertEqual(list(obs_table.T['sample_2']),
[0.0, 23.0, 8.0, 10.0, 0.0, 1.0,
11.0, 5.0, 2.0, 4.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (10, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UNINTEGRATED|g__Bacteroides.s__Bacteroides_caccae',
'UNINTEGRATED|g__Bacteroides.s__Bacteroides_finegoldii',
'UNINTEGRATED|unclassified',
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation|g__Bacteroides.s__Bacteroides_fragilis', # noqa: E501
'PWY0-1301: melibiose degradation|unclassified',
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P)|unclassified'])
self.assertEqual(
list(obs_tax['Taxon']),
['UNINTEGRATED; g__Bacteroides; s__Bacteroides_caccae',
'UNINTEGRATED; g__Bacteroides; s__Bacteroides_finegoldii',
'UNINTEGRATED; unclassified',
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_caccae', # noqa: E501
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'PWY0-1301: melibiose degradation; g__Bacteroides; s__Bacteroides_fragilis', # noqa: E501
'PWY0-1301: melibiose degradation; unclassified',
'PWY-5484: glycolysis II (from fructose-6P); g__Bacteroides; s__Bacteroides_caccae', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P); g__Bacteroides; s__Bacteroides_finegoldii', # noqa: E501
'PWY-5484: glycolysis II (from fructose-6P); unclassified'])
def test_humann_pathway_multisample_destratify(self):
_, input_table_df = self.transform_format(
HumannPathAbundanceFormat, pd.DataFrame,
'humann-pathabundance-2.tsv'
)
obs_table, obs_tax = humann_pathway(input_table_df, destratify=True)
# Assess resulting tables
self.assertEqual(obs_table.index.name, 'sample-id')
self.assertEqual(obs_table.shape, (2, 4))
self.assertEqual(list(obs_table.index), ['sample1', 'sample_2'])
self.assertEqual(
list(obs_table.columns),
['UNMAPPED',
'UNINTEGRATED',
'PWY0-1301: melibiose degradation',
'PWY-5484: glycolysis II (from fructose-6P)'])
self.assertEqual(list(obs_table.T['sample1']),
[140.0, 87.0, 57.5, 54.7])
self.assertEqual(list(obs_table.T['sample_2']),
[99.0, 42.0, 42.0, 99.0])
# Assess resulting feature metadata
self.assertEqual(obs_tax.index.name, 'Feature ID')
self.assertEqual(obs_tax.shape, (4, 1))
self.assertEqual(list(obs_tax.columns), ['Taxon'])
self.assertEqual(
list(obs_tax.index),
['UNMAPPED',
'UNINTEGRATED',
'PWY0-1301: melibiose degradation',
'PWY-5484: glycolysis II (from fructose-6P)'])
self.assertEqual(
list(obs_tax['Taxon']),
['UNMAPPED',
'UNINTEGRATED',
'PWY0-1301: melibiose degradation',
'PWY-5484: glycolysis II (from fructose-6P)'])