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.

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]
  --m-metadata-file MULTIPLE FILE
                                  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
                                  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]
  --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).
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.