# GeneAbacus Python
This repository provides Python code for [GeneAbacus](https://github.com/vejnar/GeneAbacus). Using the `profileio` module, you can import profiles exported from GeneAbacus using the *binary* format. Profiles are loaded into [Numpy](https://numpy.org) arrays, usable for analysis.
From high-throughput sequencing **mapped reads** ([SAM/BAM](https://samtools.github.io/hts-specs/)), **GeneAbacus**:
* Creates **profiles** representing coverage depth per nucleotide,
* **Counts** reads mapped within user selected features such as chromosomes or genes.
## Download
See [tags](/../../tags) page.
## Install
```bash
pip3 install geneabacus
```
## Reading profiles from Python
```python
import geneabacus.profileio
profiles = geneabacus.profileio.pfopen('profiles.bin.lz4', 'danrer_cdna_protein_coding_ensembl104.fon1.json')
```
To get a transcript profile:
```python
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
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"description": "# GeneAbacus Python\n\nThis repository provides Python code for [GeneAbacus](https://github.com/vejnar/GeneAbacus). Using the `profileio` module, you can import profiles exported from GeneAbacus using the *binary* format. Profiles are loaded into [Numpy](https://numpy.org) arrays, usable for analysis.\n\nFrom high-throughput sequencing **mapped reads** ([SAM/BAM](https://samtools.github.io/hts-specs/)), **GeneAbacus**:\n* Creates **profiles** representing coverage depth per nucleotide,\n* **Counts** reads mapped within user selected features such as chromosomes or genes.\n\n## Download\n\nSee [tags](/../../tags) page.\n\n## Install\n\n```bash\npip3 install geneabacus\n```\n\n## Reading profiles from Python\n\n```python\nimport geneabacus.profileio\nprofiles = geneabacus.profileio.pfopen('profiles.bin.lz4', 'danrer_cdna_protein_coding_ensembl104.fon1.json')\n```\n\nTo get a transcript profile:\n```python\nprofiles['ENSDART00000000486']\n# will return\narray([0., 0., 21., ..., 0., 3., 0.], dtype=float32)\n```\n\n## License\n\n*GeneAbacus* is distributed under the Mozilla Public License Version 2.0 (see /LICENSE).\n\nCopyright \u00a9 2015-2023 Charles E. Vejnar\n",
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