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.
v0.6.3: December 2024
- updated setup.py to use an entry point instead of a script
- removed
pybioscripts
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
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