README.md

sndg-bio

Bioinformatic tools

Requirements

• Linux / tested on Ubuntu distribution
• Python > 3.7 (sudo apt install python3.7)
• Python Pip (sudo apt install python3-pip)
• Docker (https://docs.docker.com/engine/install/ubuntu/)
• Virtual-env (pip3 install virtualenv) -> Recommended

Instalation

From source

git clone https://github.com/ezequieljsosa/sndg-bio.git
cd sndg-bio
virtual-env -p python3.7 env
echo export PYTHONPATH=$PYTHONPATH:$(pwd) >> env/bin/activate
source env/bin/activate
pip install -f requirements.txt
# OPTIONAL: set python env as default
echo source $(pwd)/env/bin/activate >> ${HOME}/.bashrc

Commands

Best bidirectional hits

Runs BBH algorithm using diamond-aligner

# Help python3 -m "SNDG.Sequence.BBH" -h
python3 -m "SNDG.Sequence.BBH" -f1 proteome1.faa -f2 proteome2.faa > bbhs.txt