coronavirus-visualization

Installation

Library

npm install coronavirus-visualization

Development

git clone https://github.com/stephenshank/coronavirus-visualization
cd coronavirus-visualization
yarn
conda env create -f environment.yml

Usage

NPM Library

In an environment with SASS support:

import { render_meme } from "coronavirus-visualization";
import "coronavirus-visualization/styles.scss";

render_meme(
	"/path/to/meme/json",
	"/path/to/full/fasta",
	"/path/to/base/fasta",
	"/path/to/pdb/file",
	"dom_element_id"
)

See library-consumer for a minimal working example.

Pipeline

Place a concatenated codon alignment and tree at public/input/$DATASET.fna and a PDB file at public/input/$DATASET.pdb (and make a pull request!).

Run:

snakemake public/output/$DATASET.txt

This is a dummy endpoint that will ensure all necessary file are created, running the following pipeline:

codon_fasta

Removes tree from FNA file, resulting in codon aware MSA.

amino_acid_fasta

Translate codon aware MSA.

pdb_fasta

Extracts 'A' chain from PDB file and writes to a FASTA file. See public/input/S-structure.fasta for this file.

full_alignment

Adds pdb_fasta to the translated MSA, via

mafft --add {input.pdb} {input.msa} > {output}

meme

HyPhy's MEME method.

full_dataset

Dummy file to ensure all necessary files are appropriately placed.

Development

Run

yarn develop

and visit localhost:$PORT/$DATASET.

Deployment

Set environment variable $PORT and run

npx webpack
node server.js