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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).

Options:
  --i-data ARTIFACT PATH FeatureData[Sequence]
                                  The sequences from which features should be
                                  filtered.  [required]
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  Table containing feature ids used for id-
                                  based filtering.  [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 for id-based filtering, 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 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]
  --o-filtered-data ARTIFACT PATH FeatureData[Sequence]
                                  The resulting filtered sequences.  [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_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.