ChildhoodCancerDataInitiative-CCDI_to_dbGaPy (ARCHIVED)

This repo contains a python script which takes data from a validated CCDI submission manifest and creates dbGaP submission files specifically for a CCDI project.

Table of Contents

• Python environment management
• Usage instruction

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Python environment management

A controlled virtual environment of Python is always recommanded for running any python package/script due to dependency management purpose. There are many tools that you can use to create a virtual environment, such as pyenv, virtualenv or conda. An instruction is included here on how to create a conda env with all the dependencies installed.

• Conda install

  Conda is an open source package management system and environment management system that runs on Windows, macOs, and Lunix. Here is the site of installation instruction. Please pick the right package based on your operation system.

• Create a conda env

  An environment yaml conda_environment.yml can be be found under folder envs/. To create the environment, simply run

  conda env create -f <path_to_env_yml>

  You should be able to find an environment called CCDI_to_dbGaP_env when you run

  conda env list

• Activate conda environment

  All the dependecies that the script requires should be succesfully installed within this environment. To activate the environemnt, simply run

  conda activate CCDI_to_dbGaP_env

  You should be able to see (CCDI_to_dbGaP_env) at the begining of your terminal prompt line after activation.

• Deactivate conda environment

  conda deactivate

Usage instruction

❗Note: THIS SCRIPT assumes all CONSENT to be 👉 GRU (consent number to be 1). If a CONSENT other than GRU is found, data submitter is required to fix the CONSENT encoded value in SC_DD.xlsx before submission

>> python CCDI_to_dbGaPy.py --help
usage: CCDI_to_dbGaPy.py [-h] -f FILE [-s PREVIOUS_SUBMISSION]

This script is a python version to generate dbGaP submission files using a validated CCDI
submission manifest

required arguments:
  -f FILE, --file FILE  A validated dataset file based on the template
                        CCDI_submission_metadata_template (.xlsx)

optional arguments:
  -s PREVIOUS_SUBMISSION, --previous_submission PREVIOUS_SUBMISSION
                        A previous dbGaP submission folder for the same phs_id study.

• Inputs

  The script requires a validated CCDI manifest. The previous SRA submission folder is optional.

• Outputs

  • A log file named in CCDI_to_dbGaP_<today_date>.log
  • (If the script finishes successfully) A folder named in <phs_id>_dbGaP_submission_<today_date>.

    aviator_falsetto_6_dbGaP_submission_2023-11-24/
    ├── SA_DD.xlsx
    ├── SA_DS_aviator_falsetto_6_dbGaP_submission.txt
    ├── SC_DD.xlsx
    ├── SC_DS_aviator_falsetto_6_dbGaP_submission.txt
    ├── SSM_DD.xlsx
    ├── SSM_DS_aviator_falsetto_6_dbGaP_submission.txt
    └── metadata.json
    
    1 directory, 7 files