[](https://pypi.org/project/momics/)
[](https://github.com/js2264/momics/actions/workflows/ci.yml)
[](https://app.codecov.io/gh/js2264/momics)
[](https://github.com/psf/black)
# momics
`momics` is both a revolutionary file format for efficient storage of ***multi-omics*** data, and a Python package designed to query and manipulate these files. The file format is specifically designed to handle genomic coverage tracks and sequences. The package provides an intuitive command-line interface (CLI) and a Python library for bioinformatics workflows involving genomic data.
## Install
You can install `momics` using `pip`:
```sh
pip install momics
```
Alternatively, clone this repository and install the package locally:
```sh
git clone https://github.com/js2264/momics.git
cd momics
pip install .
```
## Features
- Efficient genomic data storage: Store large genomic coverage tracks and genome reference sequences compactly.
- Multi-Range querying: Query multiple genomic regions simultaneously with high performance.
- Rich Python library: Directly access and manipulate genomic data using Python objects and methods.
- Full-fledged command-line interface (CLI): Perform common tasks such as adding new tracks, querying data, and extracting information directly from the shell.
## Usage
### CLI Commands
- Add a track:
To ingest a `.bw` genomic coverage data into a momics repository, you can use the `ingest` command:
```sh
momics ingest tracks -f bw1=path/to/file.bw path/to/momics_repo
```
- Query genomic coverage:
You can query tracks using either UCSC-style coordinates or a BED file:
```sh
momics query tracks --coordinates "chr1:1-1000" path/to/momics_repo
momics query tracks --file path/to/file.bed path/to/momics_repo
```
### Python API
In Python, you can load and query a momics repository like this:
```py
from momics.momics import Momics
# Load a Momics repository
repo = Momics("path/to/momics_repo")
# Query tracks with coordinates
df = repo.query_tracks("chr1:1-1000")
```
## Data Format
`momics` uses a custom data format that combines genomic sequences and coverage tracks in a compressed and indexed form. The format allows for rapid access to any region of the genome and supports simultaneous querying of multiple genomic regions.
## Contributing
Contributions are welcome! Please submit pull requests or issues on the GitHub repository.
This project uses `black` to format code and `ruff` for linting. We also support `pre-commit` to ensure
these have been run. To configure your local environment, please install these development dependencies and set up
the commit hooks.
## License
This project is licensed under the MIT License. See the LICENSE file for details.
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