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.

Options:
--i-table ARTIFACT PATH FeatureTable[Frequency]
The feature table from which features should
be filtered.  [required]
--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]
Metadata file or artifact viewable as
metadata. This option may be supplied
multiple times to merge metadata. Feature
metadata used with where parameter when
selecting features to retain, or with
exclude_ids when selecting features to
--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]
--o-filtered-table ARTIFACT PATH FeatureTable[Frequency]
The resulting feature table filtered by
feature.  [required if not passing --output-
dir]
--output-dir DIRECTORY          Output unspecified results to a directory
--cmd-config FILE               Use config file for command options
--verbose                       Display verbose output to stdout and/or
stderr during execution of this action.
[default: False]
--quiet                         Silence output if execution is successful
(silence is golden).  [default: False]
--citations                     Show citations and exit.
--help                          Show this message and exit.

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).
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.

Returns
-------
filtered_table : FeatureTable[Frequency]
The resulting feature table filtered by feature.