This tool is intended to rewrite all study files with new IDs based on the patient/sample ID maps. The files in the source directory must be in cBioPortal's standard file formats.
The tool takes in two files (for sample IDs, patient IDs) to map on.
python map-ids.py [-h]
-s <sample_id_map.csv>
--sample-from <original id column name in samples csv map>
--sample-to <new id column name in samples csv map>
-p patient_id_map.csv
--patient-from <original id column name in patients csv map>
--patient-to <new id column name in samples csv map>
-path <path/to/source/directory>
-dest <path/to/destination/directory>
[--drop-unknown True]
Options
-s | --sample-map: This is the path to the csv file with sample IDs to map on.
--sample-from: name of the column with original IDs in the sample-ids-map csv file
--sample-to: name of the column with new IDs to be used in the sample-ids-map csv file
-p | --patient-map: This is the path to the csv file with patient IDs to map on.
--sample-from: name of the column with original IDs in the patient-ids-map csv file
--sample-to: name of the column with new IDs to be used in the patient-ids-map csv file
-path | --source-path: This is the path to the source directory to subset from. It can be either impact or any study directory.
-dest | --destination-path: This is the destination directory to write the subsetted data to.
--drop-unknown: False by default will make script fail if it encounters an ID (sample or patient) for which there's no corresponding map (sample or patient) entry. If set to True - will silently ignore / discard that entry and continue.