grelot / vcfsynonymous

read VCF and select synonymous or non-synonymous coding variants

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 \
 --output_prefix res

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DEVELOPEMENT

download dev version

git clone [email protected]:Grelot/vcfsynonymous.git

test package

unit test

python -m pytest

real case test

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

build package

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

local installation

pip3 install .

upload pypi

twine upload dist/*

pypi installation

pip install vcfsynonymous

uninstall

pip uninstall vcfsynonymous