A library to help with protein function prediction tasks.
Follow these instructions to get this project running on your local machine for developement, testing, and running analyses locally.
###Prerequisites
In order to install this project you will need to install bioinformatics software to your system.
brew install diamond
brew install pipenv
Install other dependencies from source: cd-hit
pipenv install --dev
pipenv shell
One may run help to get a comprehensive list of the commands available:
protein-helper -h
This is an an example of a command that creates a cytoscape network representing protein similarity among a set of proteins:
protein-helper network \
--input-fasta curated_seqs.fa \
--cytoscape-cyjs curated_seqs.cyjs \
--min-percent-identity 65 \
--temp-dir cdhit_results \
--threads 4
This file can then be imported into Cytoscape for network analysis.