## Installation
npm install coronavirus-visualization```
npm install coronavirus-visualization
``
git clone https://github.com/stephenshank/coronavirus-visualization
cd coronavirus-visualization
yarn
conda env create -f environment.yml
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.
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/$DATASET.txt
This is a dummy endpoint that will ensure all necessary file are created, running the following pipeline:
#### codon_fasta
Removes tree from FNA file, resulting in codon aware MSA.
#### amino\_acid\_fasta
Translate codon aware MSA.
#### pdb_fasta
Extracts 'A' chain from PDB file and writes to a FASTA file.
See public/input/S-structure.fasta for this file.
#### full_alignment
Adds pdb_fasta to the translated MSA, via
``
mafft --add {input.pdb} {input.msa} > {output}
#### meme
HyPhy's MEME method.
#### full_dataset
Dummy file to ensure all necessary files are appropriately placed.
Run
``
yarn develop
and visit localhost:$PORT/$DATASET.
Set environment variable $PORT and run
```
npx webpack
node server.js