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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 subsample(table: biom.Table, subsampling_depth: int,
axis: str) -> biom.Table:
if axis == 'feature':
# we are transposing the table due to biocore/biom-format#759
table = table.transpose()
if len(table.ids()) < subsampling_depth:
raise ValueError('The subsampling depth exceeds the number of '
'elements on the desired axis. The maximum depth '
'is: %d.' % len(table.ids()))
# the axis is always 'sample' due to the above transpose
table = table.subsample(subsampling_depth, axis='sample', by_id=True)
# the inverted axis is always observation due to the above transpose
invaxis = 'observation'
table.filter(lambda v, i, m: v.sum() > 0, axis=invaxis)
if axis == 'feature':
# reverse the transpose necessary due to biocore/biom-format#759
table = table.transpose()
if table.is_empty():
raise ValueError('The subsampled table contains no samples or features'
' (samples/features that sum to zero after filtering'
' are automatically removed). It may be a good idea'
' to double check that your table is valid/nonempty.')
return table
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