countMembersByTaxonomy.js

#!/usr/bin/env node
var through2 = require('through2');
var byline = require('byline');
var fs = require('fs');
var argv = require('minimist')(process.argv.slice(2));

var url = argv.swagger || 'https://data.gramene.org/vitis1/swagger';
var idFile = argv.ids;
var taxa;

global.gramene = {defaultServer: url};
var gramene = require('gramene-search-client').client.grameneClient;

let GrameneTrees = require('gramene-trees-client');

var reader = byline(fs.createReadStream(idFile));

var treeFetcher = through2.obj(function(id, enc, done) {
  var that = this;
  id = id.toString();
  gramene.then(function(client) {
    client['Data access']['genetrees']({idList:[id],rows:-1}).then(function(res) {
      that.push(res.obj);
      done();
    })
  })
});

function walkTo(node, test, process) {
  if (test(node)) {
    process(node);
  }
  else {
    if (node.hasChildren()) {
      node.children.forEach(function(childNode) {
        walkTo(childNode, test, process)
      })
    }
  }
}

var checkTree = function checkTree() {
  var results = [];
	var cols = ['tree','taxa'].concat(taxa);
	results.push(cols.join("\t"));
  var transform = function(tree, enc, done) {
    let genetree = GrameneTrees.genetree.tree(tree);
		let tally = {};
		taxa.forEach(tid => tally[tid]=0);
		walkTo(
			genetree,
			node => (!node.children || node.children.length === 0 || node.model.node_type === "gene_split") && tally.hasOwnProperty(node.model.taxon_id),
			node => tally[node.model.taxon_id]++
		);
		let row = [];
		row.push(genetree._id);
		row.push(0); // number of taxa present
    for(let i=0;i<taxa.length;i++) {
      let tid = taxa[i];
			row.push(tally[tid]);
			if (tally[tid] > 0) {
				row[1]++;
			}
    }
		if (row[1] > 0) {
			results.push(row.join("\t"));
		}
    done();
  };
  
  var flush = function(done) {
	  this.push(results.join("\n"));
    done();
  }
  
  return through2.obj(transform, flush);
};


gramene.then(function(client) {
  client['Data access']['maps']({rows:-1,fl:'taxon_id,left_index'}).then(res => {
    let maps = res.obj;
    maps.sort((a, b) => a.left_index < b.left_index);
    taxa = maps.map(m => m.taxon_id);
    reader
    .pipe(treeFetcher)
    .pipe(checkTree())
    .pipe(process.stdout);
  })
});