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
DEVELOPEMENT
download dev version
git clone git@github.com: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