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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    selecting features to retain, or with `exclude-ids`
     be 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]
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).
  --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).
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.

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