pybio genomics
Project description
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 via pip and download + prepare human genome:
# install over PyPi
pip install pybio
# or install directly from this repository
pip install git+https://github.com/grexor/pybio.git@master
# 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
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
Project details
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