Fork me on GitHub

filter-features: Filter features from tableΒΆ

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.