GeneAbacus Python

This repository provides Python code for GeneAbacus. Using the profileio module, you can import profiles exported from GeneAbacus using the binary format. Profiles are loaded into Numpy arrays, usable for analysis.

From high-throughput sequencing mapped reads (SAM/BAM), GeneAbacus:

• Creates profiles representing coverage depth per nucleotide,
• Counts reads mapped within user selected features such as chromosomes or genes.

Download

See tags page.

Install

pip3 install geneabacus

Reading profiles from Python

import geneabacus.profileio
profiles = geneabacus.profileio.pfopen('profiles.bin.lz4', 'danrer_cdna_protein_coding_ensembl104.fon1.json')

To get a transcript profile:

profiles['ENSDART00000000486']
# will return
array([0., 0., 21., ..., 0., 3., 0.], dtype=float32)

License

GeneAbacus is distributed under the Mozilla Public License Version 2.0 (see /LICENSE).

Copyright © 2015-2023 Charles E. Vejnar