README.md

ChildhoodCancerDataInitiative-CCDI_to_SRAy (ARCHIVED)

This repo contains a python script which takes data from a validated CCDI submission manifest and creates an SRA submission file 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 below in your terminal

  conda env create -f <path_to_env_yml>
  

  You should be able to find an environment called CCDI_to_SRA_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_SRA_env
  

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

• Deactivate conda environment

  conda deactivate
  

Usage instruction

>> python CCDI_to_SRA.py --help
usage: CCDI_to_SRA.py [-h] -f MANIFEST -t TEMPLATE [-s PREVIOUS_SUBMISSION]

This script is a python version to generate an SRA submission file using a validated CCDI submission manifest

required arguments:
  -f MANIFEST, --manifest MANIFEST
                        A validated dataset file based on the template CCDI_submission_metadata_template (.xlsx)
  -t TEMPLATE, --template TEMPLATE
                        A dbGaP SRA metadata template, 'phsXXXXXX.xlsx'

optional arguments:
  -s PREVIOUS_SUBMISSION, --previous_submission PREVIOUS_SUBMISSION
                        A previous SRA submission file (xlsx) from the same phs_id study.

• Inputs

  The script requires a validated CCDI manifest and an SRA submission template. The previous SRA submission file is optional.

• Outputs

  • A log file named by the basename of CCDI manifest provided
  • (If the script finishes successfully) An SRA submission file named by the phs accession numnber extracted from CCDI manifest provided.

• Debug

  The script performs couple rounds of validation and verification against SRA tempaltes. Once an Error is captured, the error and additional info of errored rows will be documented in both terminal and the log file. Below is an example of error log

  09:31:05 - ERROR - 2 rows were found with one to many issue between library_ID and sample_ID
  library_IDs involved
  ('alopecias_returns_1',)
  09:31:05 - WARNING - Additional info: sample_ID and library_ID of affected rows
  ╒═════════════════════╤═════════════════════╕
  │ sample_ID           │ library_ID          │
  ╞═════════════════════╪═════════════════════╡
  │ citadel_schizoids_8 │ alopecias_returns_1 │
  ├─────────────────────┼─────────────────────┤
  │ ardebs_paupiette_1  │ alopecias_returns_1 │
  ╘═════════════════════╧═════════════════════╛