Docstring:
Usage: qiime feature-table rename-ids [OPTIONS]
Renames the sample or feature ids in a feature table using metadata to
define the new ids.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² |
PresenceAbsence³ | Composition⁴]
The table to be renamed [required]
Parameters:
--m-metadata-file METADATA
--m-metadata-column COLUMN MetadataColumn[Categorical]
A metadata column defining the new ids. Each
original id must map to a new unique id. If strict
mode is used, then every id in the original table
must have a new id. [required]
--p-axis TEXT Choices('feature', 'sample')
Along which axis to rename the ids.
[default: 'sample']
--p-strict / --p-no-strict
Whether the naming needs to be strict (each id in
the table must have a new id). Otherwise, only the
ids described in `metadata` will be renamed and the
others will keep their original id names.
[default: False]
Outputs:
--o-renamed-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² |
PresenceAbsence³ | Composition⁴]
A table which has new ids, where the ids are
replaced by values in the `metadata` column.
[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 rename_ids
Docstring:
Renames sample or feature ids in a table
Renames the sample or feature ids in a feature table using metadata to
define the new ids.
Parameters
----------
table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
The table to be renamed
metadata : MetadataColumn[Categorical]
A metadata column defining the new ids. Each original id must map to a
new unique id. If strict mode is used, then every id in the original
table must have a new id.
axis : Str % Choices('feature', 'sample'), optional
Along which axis to rename the ids.
strict : Bool, optional
Whether the naming needs to be strict (each id in the table must have a
new id). Otherwise, only the ids described in `metadata` will be
renamed and the others will keep their original id names.
Returns
-------
renamed_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
A table which has new ids, where the ids are replaced by values in the
`metadata` column.
