phylotree/bin/phylotree-reroot.js

A JavaScript library for developing applications and interactive visualizations involving [phylogenetic trees](https://en.wikipedia.org/wiki/Phylogenetic_tree), written as an extension of the [D3](http://d3js.org) [hierarchy layout](https://github.com/d3/

#!/usr/bin/env node

const fs = require("fs");
const phylotree = require("../dist/phylotree.js");
const { program } = require("commander");
const _ = require("underscore");

/*
 * phylotree reroot
 *
 * Usage:
 * phylotree reroot ./test/data/CD2-relax.new -n Horse
 *
 */

program
  .arguments("<newick>", "Input newick file")
  .requiredOption("-n --node <node>", "Node to reroot on")
  .parse(process.argv);

const options = program.opts();

if (!program.args[0]){
  throw "ERROR: Newick file is required... exiting!";
}

fs.readFile(program.args[0], (err, newickData) => {
  const tree = new phylotree.phylotree(newickData.toString());
  const node = tree.getNodeByName(options.node);
  if(_.isUndefined(node)) {
    throw new Error("Could not find node with name " + options.node);
  }
  tree.reroot(node);
  console.log(tree.getNewick());
});