Usage

Add meta data for clinical attributes as header lines to data clinical files.

Command Line

insert_clinical_metadata.py -d DIRECTORY, --directory=DIRECTORY

Example

cd path/to/brca_tcga
python insert_clinical_metadata.py -d .
rm data_clinical_patient.txt
rm data_clinical_sample.txt
mv data_clinical_patient.txt.metadata data_clinical_patient.txt
mv data_clinical_sample.txt.metadata data_clinical_sample.txt

Notes

data_clinical_patient.txt and data_clinical_sample.txt need to be presented under the existing study. clinical_attributes_metadata.txt needed under the same path. clinical_attributes_metadata.txt shall be synced with corresponding clinical data dictionary in topbraid