Metadata-Version: 2.4
Name: countess-variant-caller
Version: 0.1.1
Summary: An efficient HGVS variant caller
Author-email: Nick Moore <nick@zoic.org>
Maintainer-email: Nick Moore <nick@zoic.org>
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: fqfa~=1.3.1
Requires-Dist: rapidfuzz~=3.14.5
Provides-Extra: dev
Requires-Dist: black<24; extra == "dev"
Requires-Dist: build~=1.2.2; extra == "dev"
Requires-Dist: mypy~=2.1.0; extra == "dev"
Requires-Dist: pylint~=4.0.5; extra == "dev"
Requires-Dist: twine~=6.2.0; extra == "dev"
Requires-Dist: packaging~=25.0; extra == "dev"
Requires-Dist: pytest~=8.4.2; extra == "dev"
Dynamic: license-file

# Countess-Variant-Caller

This is a variant caller which makes HGVS variant strings from DNA sequences.
It it part of the [CountESS Project](https://github.com/CountESS-Project/)
but may be used separately.

It is intended to be fast and efficient when finding a small variation from a 
known sequence, as is common in mutational scanning experiments.

Typical usage calling DNA changes:

```
>>> from countess_variant_caller import find_variant_string

>>> find_variant_string("g.", "GATTACA", "GTTTACA")
'g.2A>T'

>>> find_variant_string("g.", "GATTACA", "GTTCAGA")
'g.[2A>T;4T>C;6C>G]'
```

It also does protein variant calling:

```
>>> from countess_variant_caller import find_variant_string

>>> find_variant_string("p.", "ATGGTTGGTTCA", "ATGGTTGGTGGTTCA")
'p.Gly3dup'

>>> find_variant_string("p.", "ATGGTTGGTTCA", "ATGGCTGCTTCA")
'p.Val2_Gly3delinsAlaAla'
```

## Contributors

* Nick Moore `nick@zoic.org`.

## License

Copyright (C) 2022- CountESS Developers under BSD 3-Clause license,
see `LICENSE.txt`.
