README

Overview

This repository is specific for SARS-CoV-2 virus submission as it has been adapted accordingly.

It contains scripts and dummy data for generating and submitting XML files to the European Nucleotide Archive (ENA). The scripts convert TSV files containing metadata into XML files with the required structure and submit the experiment, run, and sample metadata objects all in one go.

Repository Structure

this_repo
├── .gitignore
├── make-submit-xml.sh
├── exp/
│   ├── create_exp_xml.py
│   ├── exp.tsv
│   └── exp.xml
├── run/
│   ├── create_run_xml.py
│   ├── run.tsv
│   └── run.xml
├── runExpSubmit/
│   ├── add_submission.xml
│   ├── modify_submission.xml
│   ├── exp.xml
│   └── run.xml
└── samSubmit/
    ├── add_submission.xml
    ├── modify_submission.xml
    ├── create_sam_xml.py
    ├── sam.tsv
    └── sam.xml

Scripts

First set environment variables in terminal. This is a more secure way of handling credentials.

export U_NAME="your_username"
export PASS_WORD="your_password"

The wrapper script make-submit-xml.sh generates and submit (or modify existing) ENA metadata objects in XML format, using programmatic submission (https://ena-docs.readthedocs.io/en/latest/submit/reads/programmatic.html).

Usage:

make-submit-xml.sh -t  # Run in test mode (default)
make-submit-xml.sh -s  # Run in submission mode
make-submit-xml.sh -h  # Display help message

Installation

To install the required dependencies, run:

pip install lxml

create_sam_xml.py script converts the sam.tsv file into sam.xml file.

Usage:

python3 create_sam_xml.py

create_exp_xml.py script converts the exp.tsv file into an exp.xml file.

Usage:

python3 create_exp_xml.py

create_run_xml.py script converts the run.tsv file into run.xml file.

Usage:

python3 create_run_xml.py

Notes

• Ensure that the sample metadata object is submitted before running the experiment and run scripts.
• The TSV files must include all required fields for generating the metadata XML.