Bioinformatic toolkit with python (It's still under development!)
Project description
BioinformaticAnalysisTools
Introduction
A python command line toolkit for Bioinformatics and data science!
<under development>
- Author: Hua-nan ZHAO @Tsinghua University
- E-Mail: hermanzhaozzzz@gmail.com
Installation
pip install --upgrade bioat
usage
# list commands
bioat list
# check version
bioat version
# check information about bioat
bioat about
# example usage
bioat bam remove_clip --help
samtools view -h test_sorted_n.bam | bioat bam remove_clip | tail
known trouble
- You should run bioat in a rosetta env while using Apple M Silicon-Arm64 (M1/M2)
because that one dependent package
pysam
do not support this platform now. See below to use a rosetta env created by conda.
# create rosetta env
CONDA_SUBDIR=osx-64 conda create -n rosetta python
conda activate rosetta
# in rosetta env
python -c "import platform;print(platform.machine())" # should print “x86_64”
conda env config vars set CONDA_SUBDIR=osx-64
conda deactivate # need reactivate rosetta env to enable this var
conda activate rosetta
# now you can do this in this env
pip install --upgrade bioat
bioat version
Project details
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