stjudecloud-merge-counts 1.2.1
Utility for merging RNA-seq expression counts files from St. Jude Cloud.
License: MIT
Requires Python: >=3.8,<4.0
Keywords: bioinformatics,genomics,htseq

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    merge-counts
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    Utility for merging RNA-seq expression counts files from St. Jude Cloud. 
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    <a href="https://github.com/stjudecloud/merge-counts/issues/new?assignees=&labels=&template=feature_request.md&title=Descriptive%20Title&labels=enhancement">Request Feature</a>
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## 📚 Getting Started

### Installation

You can install `stjudecloud-merge-counts` using the Python Package Index ([PyPI](https://pypi.org/)).

```bash
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][contributing-md] document. 

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

```bash
# 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.

```bash
py.test
```

## 🤝 Contributing

Contributions, issues and feature requests are welcome!<br />Feel free to check [issues page](https://github.com/stjudecloud/merge-counts/issues). You can also take a look at the [contributing guide][contributing-md].

## 📝 License

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

Copyright © 2020 [St. Jude Cloud Team](https://github.com/stjudecloud).<br />

[contributing-md]: https://github.com/stjudecloud/merge-counts/blob/master/CONTRIBUTING.md
[license-md]: https://github.com/stjudecloud/merge-counts/blob/master/LICENSE.md