Fork me on GitHub

Warning

This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.

Are you looking for:

Old content beyond this point… 👴👵

split: Split one feature table into many

Docstring:

Usage: qiime feature-table split [OPTIONS]

  Splits one feature table into many feature tables, where splits are defined
  by values in metadata column.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² |
    PresenceAbsence³ | Composition⁴]
                         The table to split.                        [required]
Parameters:
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical]
                         A column defining the groups. Each unique value will
                         define a split feature table.              [required]
  --p-filter-empty-features / --p-no-filter-empty-features
                         If true, features which are not present in a split
                         feature table are dropped.            [default: True]
Outputs:
  --o-tables ARTIFACTS... Collection[FeatureTable[Frequency¹ |
    RelativeFrequency² | PresenceAbsence³ | Composition⁴]]
                         Directory where feature tables split based on
                         metadata values should be written.         [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 split

Docstring:

Split one feature table into many

Splits one feature table into many feature tables, where splits are defined
by values in metadata column.

Parameters
----------
table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
    The table to split.
metadata : MetadataColumn[Categorical]
    A column defining the groups. Each unique value will define a split
    feature table.
filter_empty_features : Bool, optional
    If true, features which are not present in a split feature table are
    dropped.

Returns
-------
tables : Collection[FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]]
    Directory where feature tables split based on metadata values should be
    written.