# pyranges

## Introduction

Pyranges is a Python library with a Rust backend for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
It enables intuitive and highly efficient pipelines for genomic analysis.

*"Finally ... This was what Python badly needed for years."* - Heng Li

## Version 1.x
This is version 1.x of pyranges. It is a complete rewrite of the original pyranges library, 
soon to replace the "default" original one (version 0). If you are a v0 user, check the migration guide 
in the documentation.

## Documentation

The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, is 
available at https://pyranges1.readthedocs.io/

## Recent Changelog

```
# 1.3.3 (13.03.26)
- nearest_ranges: treat touching intervals as nearest matches with distance 1 instead of overlapping matches
- document touching-interval nearest behavior in doctests

# 1.3.2 (27.02.26)
- pandas 3 compatibility: removed pandas<3 constraint and aligned test matrix/dependencies
- update doctests/unit test expectations to pandas 3 native formatting (including `str` dtype display)
- remove dtype display normalization workaround in table rendering
- fix pandas 3 copy-on-write/read-only array issue in coverage path used by bigwig/rle conversion
- improve groupby `prod` compatibility across pandas 2/3 edge cases

# 1.3.1 (15.02.26)
- require ruranges>=0.1.1
- remove fallback compatibility hack for old ruranges versions lacking `ruranges.numpy`
- add dtype support tests for unsigned/integer interval inputs (e.g. uint32 issue case)
```

## Install

Pyranges 1.x requires python ≥3.12. Minimal installation: 

```bash
pip install pyranges1
```

This installs and requires `ruranges>=0.1.1` automatically.

Installation including all optional dependencies:

```bash
pip install pyranges1[all]
```

Details at https://pyranges1.readthedocs.io/en/latest/installation.html


## Features

  - fast
  - memory-efficient
  - featureful
  - pythonic/pandastic

## Paper/Cite

For v1:

Stovner EB, Ticó M, Muñoz del Campo E, Pallarès-Albanell J, Chawla K, Sætrom P, Mariotti M (2025) Pyranges v1: a Python framework for ultrafast sequence interval operations.
*bioRxiv* 2025.12.11.693639; doi: https://doi.org/10.64898/2025.12.11.693639


For v0:

Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. 
*Bioinformatics 36(3):918-919*  http://dx.doi.org/10.1093/bioinformatics/btz615

## Supporting pyranges

  - most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  - use pyranges in Stack Overflow/biostars questions and answers
  - star the repo (possibly important for github visibility and as a proxy for project popularity)

## Asking for help

If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, 
or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues

## Contributing to pyranges

Pyranges accepts code contributions in form of pull request. 
For details, visit [https://pyranges1.readthedocs.io/developer_guide.html](https://pyranges1.readthedocs.io/en/latest/developer_guide.html)

## Cheatsheet
![cheatsheet](https://raw.githubusercontent.com/pyranges/pyrangeyes/for_pyranges1_1/images/pyranges_cheatsheet.png)
(The cheatsheet above was created with pyrangeyes, a companion graphical library:  https://pyrangeyes.readthedocs.io/)
