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[Sequence¹ | AlignedSequence²]
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 be `where` parameter when selecting features to retain,
merged) 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]
Outputs:
--o-filtered-data ARTIFACT FeatureData[Sequence¹ | AlignedSequence²]
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).
--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.
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[Sequence¹ | AlignedSequence²]
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[Sequence¹ | AlignedSequence²]
The resulting filtered sequences.
