Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
filter-samples: Filter samples from table¶
Docstring:
Usage: qiime feature-table filter-samples [OPTIONS]
Filter samples from table based on frequency and/or metadata. Any features
with a frequency of zero after sample filtering will also be removed. See
the filtering tutorial on https://docs.qiime2.org for additional details.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² |
PresenceAbsence³ | Composition⁴]
The feature table from which samples should be
filtered. [required]
Parameters:
--p-min-frequency INTEGER
The minimum total frequency that a sample must have
to be retained. [default: 0]
--p-max-frequency INTEGER
The maximum total frequency that a sample can have
to be retained. If no value is provided this will
default to infinity (i.e., no maximum frequency
filter will be applied). [optional]
--p-min-features INTEGER
The minimum number of features that a sample must
have to be retained. [default: 0]
--p-max-features INTEGER
The maximum number of features that a sample can
have to be retained. If no value is provided this
will default to infinity (i.e., no maximum feature
filter will be applied). [optional]
--m-metadata-file METADATA...
(multiple Sample metadata used with `where` parameter when
arguments will be selecting samples to retain, or with `exclude-ids`
merged) when selecting samples to discard. [optional]
--p-where TEXT SQLite WHERE clause specifying sample metadata
criteria that must be met to be included in the
filtered feature table. If not provided, all samples
in `metadata` that are also in the feature table will
be retained. [optional]
--p-exclude-ids / --p-no-exclude-ids
If true, the samples selected by `metadata` or
`where` parameters will be excluded from the filtered
table instead of being retained. [default: False]
--p-filter-empty-features / --p-no-filter-empty-features
If true, features which are not present in any
retained samples are dropped. [default: True]
--p-allow-empty-table / --p-no-allow-empty-table
If true, the filtered table may be empty. Default
behavior is to raise an error if the filtered table
is empty. [default: False]
Outputs:
--o-filtered-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency²
| PresenceAbsence³ | Composition⁴]
The resulting feature table filtered by sample.
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Examples:
# ### example: filter to subject1
qiime feature-table filter-samples \
--i-table feature-table.qza \
--m-metadata-file sample-metadata.tsv \
--p-where '[subject]="subject-1"' \
--o-filtered-table filtered-table.qza
# ### example: filter to skin
qiime feature-table filter-samples \
--i-table feature-table.qza \
--m-metadata-file sample-metadata.tsv \
--p-where '[body-site] IN ("left palm", "right palm")' \
--o-filtered-table filtered-table.qza
# ### example: filter to subject1 gut
qiime feature-table filter-samples \
--i-table feature-table.qza \
--m-metadata-file sample-metadata.tsv \
--p-where '[subject]="subject-1" AND [body-site]="gut"' \
--o-filtered-table filtered-table.qza
# ### example: filter to gut or abx
qiime feature-table filter-samples \
--i-table feature-table.qza \
--m-metadata-file sample-metadata.tsv \
--p-where '[body-site]="gut" OR [reported-antibiotic-usage]="Yes"' \
--o-filtered-table filtered-table.qza
# ### example: filter to subject1 not gut
qiime feature-table filter-samples \
--i-table feature-table.qza \
--m-metadata-file sample-metadata.tsv \
--p-where '[subject]="subject-1" AND NOT [body-site]="gut"' \
--o-filtered-table filtered-table.qza
# ### example: filter min features
qiime feature-table filter-samples \
--i-table feature-table.qza \
--p-min-features 10 \
--o-filtered-table filtered-table.qza
# ### example: filter min frequency
qiime feature-table filter-samples \
--i-table feature-table.qza \
--p-min-frequency 1500 \
--o-filtered-table filtered-table.qza
Import:
from qiime2.plugins.feature_table.methods import filter_samples
Docstring:
Filter samples from table
Filter samples from table based on frequency and/or metadata. Any features
with a frequency of zero after sample filtering will also be removed. See
the filtering tutorial on https://docs.qiime2.org for additional details.
Parameters
----------
table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
The feature table from which samples should be filtered.
min_frequency : Int, optional
The minimum total frequency that a sample must have to be retained.
max_frequency : Int, optional
The maximum total frequency that a sample can have to be retained. If
no value is provided this will default to infinity (i.e., no maximum
frequency filter will be applied).
min_features : Int, optional
The minimum number of features that a sample must have to be retained.
max_features : Int, optional
The maximum number of features that a sample can have to be retained.
If no value is provided this will default to infinity (i.e., no maximum
feature filter will be applied).
metadata : Metadata, optional
Sample metadata used with `where` parameter when selecting samples to
retain, or with `exclude_ids` when selecting samples to discard.
where : Str, optional
SQLite WHERE clause specifying sample metadata criteria that must be
met to be included in the filtered feature table. If not provided, all
samples in `metadata` that are also in the feature table will be
retained.
exclude_ids : Bool, optional
If true, the samples selected by `metadata` or `where` parameters will
be excluded from the filtered table instead of being retained.
filter_empty_features : Bool, optional
If true, features which are not present in any retained samples are
dropped.
allow_empty_table : Bool, optional
If true, the filtered table may be empty. Default behavior is to raise
an error if the filtered table is empty.
Returns
-------
filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
The resulting feature table filtered by sample.