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filter-seqs: Filter features from sequencesΒΆ

Docstring:

Usage: qiime feature-table filter-seqs [OPTIONS]

  Filter features from sequences based on a feature table or metadata. See
  the filtering tutorial on https://docs.qiime2.org for additional details.
  This method can filter based on ids in a table or a metadata file, but not
  both (i.e., the table and metadata options are mutually exclusive).

Inputs:
  --i-data ARTIFACT FeatureData[Sequence]
                       The sequences from which features should be filtered.
                                                                    [required]
  --i-table ARTIFACT FeatureTable[Frequency]
                       Table containing feature ids used for id-based
                       filtering.                                   [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple          Feature metadata used for id-based filtering, with
     arguments will    `where` parameter when selecting features to retain, or
     be merged)        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 sequences will be
                       retained.                                    [optional]
  --p-exclude-ids / --p-no-exclude-ids
                       If true, the features selected by the `metadata` (with
                       or without the `where` parameter) or `table` parameter
                       will be excluded from the filtered sequences instead of
                       being retained.                        [default: False]
Outputs:
  --o-filtered-data ARTIFACT FeatureData[Sequence]
                       The resulting filtered sequences.            [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_seqs

Docstring:

Filter features from sequences

Filter features from sequences based on a feature table or metadata. See
the filtering tutorial on https://docs.qiime2.org for additional details.
This method can filter based on ids in a table or a metadata file, but not
both (i.e., the table and metadata options are mutually exclusive).

Parameters
----------
data : FeatureData[Sequence]
    The sequences from which features should be filtered.
table : FeatureTable[Frequency], optional
    Table containing feature ids used for id-based filtering.
metadata : Metadata, optional
    Feature metadata used for id-based filtering, 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 sequences will be retained.
exclude_ids : Bool, optional
    If true, the features selected by the `metadata` (with or without the
    `where` parameter) or `table` parameter will be excluded from the
    filtered sequences instead of being retained.

Returns
-------
filtered_data : FeatureData[Sequence]
    The resulting filtered sequences.