merge-counts

Utility for merging RNA-seq expression counts files from St. Jude Cloud.

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📚 Getting Started

Installation

You can install stjudecloud-merge-counts using the Python Package Index (PyPI).

pip install stjudecloud-merge-counts

Usage

stjudecloud-merge-counts has 4 subcommands:

• concordance-test - Performs a recursive and sequential merge and verifies that the results are concordant.
• metadata - Compiles file metadata into a tab-delimited matrix.
• recursive - Merges count files in a recursive, divide-and-conquer strategy.
• sequential - Merges count files sequentially. This method requires significantly more time than the recursive approach.

All four subcommands require a set of DNAnexus file IDs to be supplied as commandline arguments.

For feature counts vended from St. Jude Cloud platform, the following example will merge the vended counts into a tab-delimited matrix. Replace project-G2KfyQ09XB5BBKKf1BXx9ZkK with the project identifier for your DNAnexus project containing feature counts.

dx ls --brief project-G2KfyQ09XB5BBKKf1BXx9ZkK:/immediate/FEATURE_COUNTS/ | xargs stjudecloud-merge-counts recursive

🖥️ Development

If you are interested in contributing to the code, please first review our CONTRIBUTING.md document.

To bootstrap a development environment, please use the following commands.

# Clone the repository
git clone git@github.com:stjudecloud/merge-counts.git
cd merge-counts

# Install the project using poetry
poetry install

🚧️ Tests

merge-counts provides a (currently patchy) set of tests — both unit and end-to-end.

py.test

🤝 Contributing

Contributions, issues and feature requests are welcome!
Feel free to check issues page. You can also take a look at the contributing guide.

📝 License

This project is licensed under the MIT License—see the LICENSE.md file for details.

Copyright © 2020 St. Jude Cloud Team.