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:

pip install momics

Alternatively, clone this repository and install the package locally:

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:

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:

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:

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.