ucsc-xena-client/dist/findIntrons.js

UCSC Xena Client. Functional genomics visualizations.

'use strict';

// Find contiguous intron regions across a set of transcripts, i.e.
// regions without any exons. These are not, strictly speaking, 'introns',
// but intronic regions in every transcript.

function _toArray(arr) { return Array.isArray(arr) ? arr : Array.from(arr); }

var _ = require('./underscore_ext');

// Create a group with one exon
var initGroup = function initGroup(exon) {
	return {
		start: exon.start,
		end: exon.end,
		exons: [exon]
	};
};

var push = function push(arr, v) {
	return arr.push(v), arr;
};

// Update a group with an overlapping exon
function updateGroup(group, exon) {
	var newEnd = group.end < exon.end ? exon.end : group.end;
	return {
		start: group.start,
		end: newEnd,
		exons: push(group.exons, exon)
	};
}

function mergeTop(groups, exon) {
	var len = groups.length - 1,
	    last = groups[len];
	if (last.start <= exon.end && exon.start <= last.end) {
		groups[len] = updateGroup(last, exon);
	} else {
		groups.push(initGroup(exon));
	}
	return groups;
}

// findIntrons(exons :: [[{start, end}, {start, end}, ...], ...]) ::
//    [{start, end, exons: [...]}, ...]
//
// exons in the returned groups are sorted by start position.
function exonGroups(exons) {
	if (exons.length < 1) {
		return [];
	}
	var sorted = _.sortBy(exons, 'start'),
	    _sorted = _toArray(sorted),
	    first = _sorted[0],
	    rest = _sorted.slice(1);

	return rest.reduce(mergeTop, [initGroup(first)]);
}

function intronRegions(groups) {
	return groups.slice(1).map(function (_ref, i) {
		var start = _ref.start,
		    end = _ref.end;
		return [groups[i].end, start];
	});
}

// exons(transcripts :: [{exonStarts, exonEnds}, ...]) :: [{start, end}, ...]
function allExons(transcripts) {
	return _.flatmap(transcripts, function (_ref2) {
		var exonStarts = _ref2.exonStarts,
		    exonEnds = _ref2.exonEnds;
		return _.mmap(exonStarts, exonEnds, function (start, end) {
			return { start: start, end: end };
		});
	});
}

module.exports = {
	allExons: allExons,
	exonGroups: exonGroups,
	intronRegions: intronRegions
};