def alpha(table: biom.Table):
"""
:param table:
:return:
"""
if table.is_empty():
raise ValueError("The provided table object is empty")
table = get_biom_table(table)
alpha_diversities = []
counts = table.matrix_data.toarray().astype(float).T
sample_ids = table.ids(axis='sample')
sample_metadata = dict(zip(table.ids(), table.metadata()))
for metric in ALPHA_DIVERSITY_METHODS:
result = alpha_diversity(metric=metric, counts=counts, ids=sample_ids)
result.name = metric
alpha_diversities.append(result)
aggregated_diversity_results = aggregate_results(alpha_diversities,
sample_ids)
formatted_diversity_results = _format_alpha_results_to_json(
aggregated_diversity_results, sample_metadata)
return formatted_diversity_results
def biom_to_table(table: biom.Table):
"""Convert a BIOM table into table components.
Parameters
----------
table : biom.Table
BIOM table to convert.
Returns
-------
tuple of
list of list
Profile data.
list
Observation IDs.
list
Sample IDs.
list of dict
Observation metadata.
"""
return (table.matrix_data.toarray().astype(int).tolist(),
table.ids('observation').tolist(), table.ids('sample').tolist(),
list(map(dict,
table.metadata(axis='observation') or ())))
def test_add_metacol(self):
obs = prep_table({
'S1': {
'G1': 4,
'G2': 5,
'G3': 8,
'G4': 0,
'G5': 3
},
'S2': {
'G1': 1,
'G2': 8,
'G3': 0,
'G4': 7,
'G5': 4
},
'S3': {
'G1': 0,
'G2': 2,
'G3': 3,
'G4': 5,
'G5': 0
}
})
self.assertListEqual(obs[3], [{}] * 5)
ob2 = Table(*map(np.array, obs))
# regular table
rankdic = {'G1': 'S', 'G2': 'S', 'G3': 'F', 'G4': 'O', 'G5': 'P'}
add_metacol(obs, rankdic, 'Rank')
exp = [{
'Rank': 'S'
}, {
'Rank': 'S'
}, {
'Rank': 'F'
}, {
'Rank': 'O'
}, {
'Rank': 'P'
}]
self.assertListEqual(obs[3], exp)
# BIOM table
add_metacol(ob2, rankdic, 'Rank')
self.assertListEqual(list(map(dict, ob2.metadata(axis='observation'))),
exp)
# unordered, missing value, append
namedic = {
'G1': 'Proteo',
'G3': 'Actino',
'G2': 'Firmic',
'G4': 'Bacter'
}
add_metacol(obs, namedic, 'Name', missing='X')
exp = [{
'Rank': 'S',
'Name': 'Proteo'
}, {
'Rank': 'S',
'Name': 'Firmic'
}, {
'Rank': 'F',
'Name': 'Actino'
}, {
'Rank': 'O',
'Name': 'Bacter'
}, {
'Rank': 'P',
'Name': 'X'
}]
self.assertListEqual(obs[3], exp)
add_metacol(ob2, namedic, 'Name', missing='X')
self.assertListEqual(list(map(dict, ob2.metadata(axis='observation'))),
exp)
def test_biom_add_metacol(self):
obs = Table(*map(
np.array,
prep_table({
'S1': {
'G1': 4,
'G2': 5,
'G3': 8,
'G4': 0,
'G5': 3
},
'S2': {
'G1': 1,
'G2': 8,
'G3': 0,
'G4': 7,
'G5': 4
},
'S3': {
'G1': 0,
'G2': 2,
'G3': 3,
'G4': 5,
'G5': 0
}
})))
self.assertIsNone(obs.metadata(axis='observation'))
rankdic = {'G1': 'S', 'G2': 'S', 'G3': 'F', 'G4': 'O', 'G5': 'P'}
biom_add_metacol(obs, rankdic, 'Rank')
exp = [{
'Rank': 'S'
}, {
'Rank': 'S'
}, {
'Rank': 'F'
}, {
'Rank': 'O'
}, {
'Rank': 'P'
}]
self.assertListEqual(list(map(dict, obs.metadata(axis='observation'))),
exp)
namedic = {
'G1': 'Proteo',
'G3': 'Actino',
'G2': 'Firmic',
'G4': 'Bacter'
}
biom_add_metacol(obs, namedic, 'Name', missing='X')
exp = [{
'Rank': 'S',
'Name': 'Proteo'
}, {
'Rank': 'S',
'Name': 'Firmic'
}, {
'Rank': 'F',
'Name': 'Actino'
}, {
'Rank': 'O',
'Name': 'Bacter'
}, {
'Rank': 'P',
'Name': 'X'
}]
self.assertListEqual(list(map(dict, obs.metadata(axis='observation'))),
exp)