semvec/pypi-packages huggingface dataset:
vcfsynonymous 0.2.0
Detect synonymous genetic variants in VCF
License: MIT

# VCFSYNONYMOUS

[![PyPI version](https://badge.fury.io/py/vcfsynonymous.svg)](https://badge.fury.io/py/vcfsynonymous)
[![license](https://img.shields.io/pypi/l/vcfsynonymous.svg)](https://pypi.org/project/vcfsynonymous/)
[![Build Status](https://travis-ci.com/Grelot/vcfsynonymous.svg?branch=main)](https://travis-ci.com/Grelot/vcfsynonymous)
[![Supported Python Versions](https://img.shields.io/pypi/pyversions/vcfsynonymous.svg)](https://pypi.python.org/pypi/vcfsynonymous)



Giving `.gff3` and `.fasta` files of a genome and `.vcf` detected SNPs onto this genome, **VCFSYNONYMOUS** returns two `.vcf` files. The first one contains synonymous SNPs and the second one contains non-synonymous SNPs.


## INSTALLATION

```
pip3 install vcfsynonymous
```

## GET STARTED

```
vcfsynonymous --vcf tests/data/sample.vcf \
 --genome tests/data/genome.fasta \
 --annotation tests/data/genome.gff3
```


___________________________________________________________

```
python -m vcfsynonymous --vcf tests/data/sample.vcf \
 --genome tests/data/genome.fasta \
 --annotation tests/data/genome.gff3 \
 --output_prefix res
```


### upload package

```
pip3 uninstall vcfsynonymous
rm -rf build/
rm -rf dist/
rm -rf vcfsynonymous.egg-info/
python setup.py sdist bdist_wheel
pip3 install .

twine upload dist/*
```