ucsc-xena-client/dist/parsePos.js

UCSC Xena Client. Functional genomics visualizations.

'use strict';

var _ = require('./underscore_ext');
var unicode = require('./unicode_utils');
var chromInfo = require('./chromInfo');
var centromere = require('./centromere');

var toInt = function toInt(x) {
	return parseInt(x, 10);
};
var clip = function clip(len, x) {
	return x < 1 ? 1 : x > len ? len : x;
};
var M = 1000 * 1000;

module.exports = function (text, assembly) {
	// strip spaces, cvt to lower, match chr1:2-chr3:4 format
	text = unicode.normalize(text).replace(/ /g, '').toLowerCase();
	var pos = text.match(/^(chr[0-9xyXY]+)([pq]?)(:([0-9,]+)(-([0-9,]+))?)?$/);
	if (pos) {
		var chrom = pos[1].replace(/x/, 'X').replace(/y/, 'Y'),
		    cm = _.getIn(centromere, [assembly, chrom]),
		    maxEnd = _.getIn(chromInfo, [assembly, chrom], 250 * M),
		    baseStart = void 0,
		    baseEnd = void 0;
		if (pos[3] !== undefined) {
			if (pos[6] !== undefined) {
				baseEnd = clip(maxEnd, toInt(pos[6].replace(/,/g, '')));
				baseStart = clip(baseEnd, toInt(pos[4].replace(/,/g, '')));
			} else {
				baseStart = clip(maxEnd, toInt(pos[4].replace(/,/g, '')));
				baseEnd = baseStart;
			}
		} else if (cm && pos[2] === 'p') {
			baseStart = 1;
			baseEnd = cm - 1;
		} else if (cm && pos[2] === 'q') {
			baseStart = cm;
			baseEnd = maxEnd;
		} else {
			baseStart = 1;
			baseEnd = maxEnd;
		}
		return { chrom: chrom, baseStart: baseStart, baseEnd: baseEnd };
	}
};