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.

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.

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

pybio is developed and supported by Gregor Rot.

Use the issues page to report issues and leave suggestions.

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