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rename-ids: Renames sample or feature ids in a table¶
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.