abstar
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
- Source code: github.com/brineylab/abstar
- Documentation: abstar.readthedocs.org
- Download: pypi.python.org/pypi/abstar
- Docker: hub.docker.com/r/brineylab/datascience/
install
pip install abstar
use
To run abstar on a single FASTA or FASTQ file, you need to supply the input file and the project directory (into which output and logs will be written):
abstar path/to/sequences.fasta path/to/project_directory
To iteratively run abstar on all files in an input directory, pass a directory containing FASTA or FASTQ files instead of the path to a single file:
abstar path/to/input_directory path/to/project_directory
additional options
abstar contains a number of additional options and tools, including merging paired-end reads, parsing unique molecular identifiers (UMIs), and building/using custom germline databases. These are described in the abstar documentation.
api
Most core abstar functions are available through a Python API, making it easier to run abstar as a component of integrated analysis pipelines or to run abstar interactively (e.g. in a Jupyter notebook). See the abstar documentation for more detail about the API.
testing
You can run the complete abstar test suite by first installing pytest:
pip install pytest
followed by:
git clone https://github.com/brineylab/abstar
cd abstar
pytest
This test suite is automatically run after every commit, and is tested against all supported versions of Python.
requirements
Python 3.10+
abutils
click
matplotlib
numpy
pandas
parasail
polars
pyarrow
pytest
1 maintainer
Metadata
1 maintainer
Release files for abstar 0.8.0
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| File | Size | Uploaded | |
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| abstar-0.8.0.tar.gz | 640.0 kB | Details |
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|---|---|---|---|---|
| abstar-0.8.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.4 MB
Release files / abstar-0.8.0.tar.gz
| Download URL | abstar-0.8.0.tar.gz |
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| Size | 640.0 kB |
| Tags | Source |
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| Tags | Python 3 |
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