Metadata-Version: 2.1
Name: hictkpy
Version: 0.0.4
Summary: Blazing fast toolkit to work with .hic and .cool files
Author-Email: Roberto Rossini <roberros@uio.no>
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.9
Requires-Dist: numpy
Requires-Dist: pandas!=2.2.0,>=2.1.0
Requires-Dist: scipy
Requires-Dist: pytest>=6.0; extra == "test"
Provides-Extra: test
Description-Content-Type: text/markdown

<!--
Copyright (C) 2023 Roberto Rossini <roberros@uio.no>

SPDX-License-Identifier: MIT
-->

# hictkpy

[![License](https://img.shields.io/badge/license-MIT-green)](./LICENSE)
[![CI](https://github.com/paulsengroup/hictkpy/actions/workflows/pip.yml/badge.svg)](https://github.com/paulsengroup/hictkpy/actions/workflows/pip.yml)
[![Download from Bioconda](https://img.shields.io/conda/vn/bioconda/hictkpy?label=bioconda&logo=Anaconda)](https://anaconda.org/bioconda/hictkpy)
[![docs](https://readthedocs.org/projects/hictkpy/badge/?version=latest)](https://hictkpy.readthedocs.io/en/latest/?badge=latest)
[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8220299.svg)](https://doi.org/10.5281/zenodo.8220299)
---

Python bindings for hictk, a blazing fast toolkit to work with .hic and .cool files.

## Installing hictkpy

hictkpy can be installed in various ways. The simples method is using pip: `pip install hictkpy`.

Refer to [Installation](https://hictkpy.readthedocs.io/en/latest/installation.html) for alternative methods.

## Using hictkpy

```python3
import hictkpy

path_to_clr = "file.mcool"  # "file.hic"

clr = hictkpy.File(path_to_clr, 100_000)
sel = clr.fetch("chr1")

df = sel.to_df()     # Get interactions as a pd.DataFrame
m1 = sel.to_numpy()  # Get interactions as a numpy matrix
m2 = sel.to_coo()    # Get interactions as a scipy.sparse.coo_matrix
```

For more detailed examples refer to [Quickstart](https://hictkpy.readthedocs.io/en/latest/quickstart.html).

The complete documentation for hictkpy API is available [here](https://hictkpy.readthedocs.io/en/latest/hictkpy.html).

## Citing

If you use hictkpy in you reaserch, please cite the following publication:

Roberto Rossini, Jonas Paulsen hictk: blazing fast toolkit to work with .hic and .cool files.
_bioRxiv_ __2023.11.26.568707__. [https://doi.org/10.1101/2023.11.26.568707](https://doi.org/10.1101/2023.11.26.568707)

<details>
<summary>BibTex</summary>

```bibtex
@article {hictk,
	author = {Roberto Rossini and Jonas Paulsen},
	title = {hictk: blazing fast toolkit to work with .hic and .cool files},
	elocation-id = {2023.11.26.568707},
	year = {2023},
	doi = {10.1101/2023.11.26.568707},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707},
	eprint = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707.full.pdf},
	journal = {bioRxiv}
}
```

</details>
