merge-counts
Utility for merging RNA-seq expression counts files from St. Jude Cloud.
Request Feature
·
Report Bug
·
📚 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 arecursive
andsequential
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.