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).

Metadata

Release files for geneabacus 0.3.2

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Source distribution for geneabacus 0.3.2
File	Size	Uploaded	Provenance
geneabacus-0.3.2.tar.gz	9.2 kB	Jun 26, 2023	Without provenance	Details

Release files / geneabacus-0.3.2.tar.gz

Download URL	geneabacus-0.3.2.tar.gz
Size	9.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`1bde089f9f8c243cfa0b68ba366fc05e3d6d43fd537d5eef7e0a93d584426a74`
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Upload date	Jun 26, 2023
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Uploaded via	`twine/4.0.2 CPython/3.11.3`

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