Metadata-Version: 2.4
Name: abstar
Version: 0.7.4
Summary: Germline assignment and annotation of AIRR data. Scalable from a single sequence to billions of sequences.
Author-email: Bryan Briney <briney@scripps.edu>
License: The MIT License (MIT)
        
        Copyright (c) 2025 brineylab @ scripps
        
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Project-URL: Homepage, https://github.com/brineylab/abstar
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: abutils>=0.5.1
Requires-Dist: click
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: parasail
Requires-Dist: polars
Requires-Dist: pyarrow
Requires-Dist: pytest
Dynamic: license-file

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# abstar  
  
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.  
  
  - Source code: [github.com/brineylab/abstar](https://github.com/brineylab/abstar)  
  - Documentation: [abstar.readthedocs.org](http://abstar.readthedocs.org)  
  - Download: [pypi.python.org/pypi/abstar](https://pypi.python.org/pypi/abstar)  
  - Docker: [hub.docker.com/r/brineylab/datascience/](https://hub.docker.com/r/brineylab/datascience/)  
  
## install  
``` bash
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):  
``` bash
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:  
``` bash
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](http://abstar.readthedocs.org).  
  

## 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](http://abstar.readthedocs.org) for more detail about the API.  
  

## testing  
You can run the complete `abstar` test suite by first installing `pytest`:
``` bash
pip install pytest
```

followed by:

``` bash
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  
