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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, 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 biom
def rarefy(table: biom.Table, sampling_depth: int,
with_replacement: bool = False) -> biom.Table:
if with_replacement:
table = table.filter(lambda v, i, m: v.sum() >= sampling_depth,
inplace=False, axis='sample')
table = table.subsample(sampling_depth, axis='sample', by_id=False,
with_replacement=with_replacement)
if table.is_empty():
raise ValueError('The rarefied table contains no samples or features. '
'Verify your table is valid and that you provided a '
'shallow enough sampling depth.')
return table
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