coronavirus-visualization

Installation

$3

``
npm install coronavirus-visualization
`

$3

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

Usage

$3

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.

$3

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.

$3

Run

`
yarn develop
`

and visit localhost:$PORT/$DATASET.

Deployment

Set environment variable $PORT and run

`
npx webpack
node server.js
``