pybio 0.3.13

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:

pip install pybio
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

v0.3.12: November 2023

• updated docs