pybio

pybio: basic genomics toolset

pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs. The primary objective of pybio is to simplify genome management. It achieves this by providing automatic download of Ensembl genome assemblies and annotation, provides Python genomic feature search and sequence retrieval from the managed genomes, STAR indexing and mapping and more.

Quick Start

Install and download + prepare human genome:

# Option 1: install over PyPi
pip install pybio

# Option 2: install from this repository
pip install git+https://github.com/grexor/pybio.git@master

# Option 3: use over singularity / apptainer / Docker (only if you don't need python imports)
singularity run docker://ghcr.io/grexor/pybio:master pybio

# Download and process homo sapiens genome
pybio genome homo_sapiens

Search genome features (exons, transcripts, genes) from Python:

import pybio
result = pybio.core.genomes.annotate("homo_sapiens", "1", "+", 11012344)
genes, transcripts, exons, UTR5, UTR3 = result

Retrieve genomic sequences from Python:

import pybio
seq = pybio.core.genomes.seq("homo_sapiens", "1", "+", 450000, -20, 20)

Check documentation for more examples.

Documentation

PDF reference manual
Google docs of the above PDF (comment if you like)

Authors

pybio is developed and supported by Gregor Rot.

Issues and Suggestions

Use the issues page to report issues and leave suggestions.

Change log

0.8.4: 28 October 2025

moved os.system to subprocess
fixed direct calling of python3 to sys.executable

0.8: May 2025

aimux: added short-read paired end sequencing demultiplexing tool

0.7: February 2025

alignIntronMax for STAR
other small fixes

v0.6.3: December 2024

updated setup.py to use an entry point instead of a script
removed pybio scripts

v0.6: November 2024

updated Ensembl search and genome versioning offline
updated custom genome interface

v0.5: May 2024

refreshed Ensembl (112) and Ensembl Genomes (58) database

v0.4: April 2024

refreshed Ensembl (111) and Ensembl Genomes (58) database

v0.3.12: released in November 2023

updated docs

Citation

If you are using pybio in your research, please cite:

Rot, G., Wehling, A., Schmucki, R., Berntenis, N., Zhang, J. D., & Ebeling, M. (2024)
splicekit : an integrative toolkit for splicing analysis from short-read RNA-seq
Bioinformatics Advances, 4(1). https://doi.org/10.1093/bioadv/vbae121

Metadata

Release files for pybio 0.8.8

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pybio 0.8.8
File	Size	Uploaded
pybio-0.8.8.tar.gz	399.1 kB	Sep 17, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for pybio 0.8.8
File	Interpreter	ABI	Platform	Reset
pybio-0.8.8-py3-none-any.whl 44.8 kB Sep 17, 2026	Python 3	none	any	Details

Total release size: 443.9 kB

Release files / pybio-0.8.8.tar.gz

Download URL	pybio-0.8.8.tar.gz
Size	399.1 kB
Tags	Source
SHA-256 checksum How to use checksums	`91f4a444d67e6b5c18dd937e97613e22c048c45dab94b91ea9bc23112af0aa33`
BLAKE2b-256 checksum How to use checksums	`bf0ea3a45b5894cd7bdffe062dadbaafa253de8e0fc279a47d8f5419273b8bd1`
Upload date	Sep 17, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.2`

Release files / pybio-0.8.8-py3-none-any.whl

Download URL	pybio-0.8.8-py3-none-any.whl
Size	44.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`21c5a85b2ba231292e142510451c09cceab11618c944d286bb0dc8e1f24f7d74`
BLAKE2b-256 checksum How to use checksums	`7a8d06777286f714d91629889debd637d9c387d5faa03966914648f43c2df93c`
Upload date	Sep 17, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.2`