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filter-features: Filter features from table¶
Docstring:
Usage: qiime feature-table filter-features [OPTIONS]
Filter features from table based on frequency and/or metadata. Any samples
with a frequency of zero after feature filtering will also be removed. See
the filtering tutorial on https://docs.qiime2.org for additional details.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table from which features should be
filtered. [required]
Parameters:
--p-min-frequency INTEGER
The minimum total frequency that a feature must have
to be retained. [default: 0]
--p-max-frequency INTEGER
The maximum total frequency that a feature 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-samples INTEGER
The minimum number of samples that a feature must be
observed in to be retained. [default: 0]
--p-max-samples INTEGER
The maximum number of samples that a feature can be
observed in to be retained. If no value is provided
this will default to infinity (i.e., no maximum
sample filter will be applied). [optional]
--m-metadata-file METADATA...
(multiple Feature metadata used with `where` parameter when
arguments will be selecting features to retain, or with `exclude-ids`
merged) when selecting features to discard. [optional]
--p-where TEXT SQLite WHERE clause specifying feature metadata
criteria that must be met to be included in the
filtered feature table. If not provided, all features
in `metadata` that are also in the feature table will
be retained. [optional]
--p-exclude-ids / --p-no-exclude-ids
If true, the features selected by `metadata` or
`where` parameters will be excluded from the filtered
table instead of being retained. [default: False]
--p-filter-empty-samples / --p-no-filter-empty-samples
If true, drop any samples where none of the retained
features are present. [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[Frequency]
The resulting feature table filtered by feature.
[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 features min samples
qiime feature-table filter-features \
--i-table feature-table.qza \
--p-min-samples 2 \
--o-filtered-table filtered-table.qza
Import:
from qiime2.plugins.feature_table.methods import filter_features
Docstring:
Filter features from table
Filter features from table based on frequency and/or metadata. Any samples
with a frequency of zero after feature filtering will also be removed. See
the filtering tutorial on https://docs.qiime2.org for additional details.
Parameters
----------
table : FeatureTable[Frequency]
The feature table from which features should be filtered.
min_frequency : Int, optional
The minimum total frequency that a feature must have to be retained.
max_frequency : Int, optional
The maximum total frequency that a feature 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_samples : Int, optional
The minimum number of samples that a feature must be observed in to be
retained.
max_samples : Int, optional
The maximum number of samples that a feature can be observed in to be
retained. If no value is provided this will default to infinity (i.e.,
no maximum sample filter will be applied).
metadata : Metadata, optional
Feature metadata used with `where` parameter when selecting features to
retain, or with `exclude_ids` when selecting features to discard.
where : Str, optional
SQLite WHERE clause specifying feature metadata criteria that must be
met to be included in the filtered feature table. If not provided, all
features in `metadata` that are also in the feature table will be
retained.
exclude_ids : Bool, optional
If true, the features selected by `metadata` or `where` parameters will
be excluded from the filtered table instead of being retained.
filter_empty_samples : Bool, optional
If true, drop any samples where none of the retained features are
present.
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[Frequency]
The resulting feature table filtered by feature.