added a bed counter
I know there are tools for this purpose, but they don't quite meet my exact need.
This commit is contained in:
Heng Li
parent
7b5a601d48
commit
bf72969ab1
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@ -0,0 +1,211 @@
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/*******************************
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* Command line option parsing *
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*******************************/
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var getopt = function(args, ostr) {
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var oli; // option letter list index
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if (typeof(getopt.place) == 'undefined')
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getopt.ind = 0, getopt.arg = null, getopt.place = -1;
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if (getopt.place == -1) { // update scanning pointer
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if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
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getopt.place = -1;
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return null;
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}
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if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
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++getopt.ind;
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getopt.place = -1;
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return null;
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}
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}
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var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
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if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
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if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
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if (getopt.place < 0) ++getopt.ind;
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return '?';
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}
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if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
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getopt.arg = null;
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if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
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} else { // need an argument
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if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
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getopt.arg = args[getopt.ind].substr(getopt.place);
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else if (args.length <= ++getopt.ind) { // no arg
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getopt.place = -1;
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if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
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return '?';
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} else getopt.arg = args[getopt.ind]; // white space
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getopt.place = -1;
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++getopt.ind;
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}
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return optopt;
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}
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/***********************
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* Interval operations *
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***********************/
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Interval = {};
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Interval.sort = function(a)
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{
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if (typeof a[0] == 'number')
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a.sort(function(x, y) { return x - y });
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else a.sort(function(x, y) { return x[0] != y[0]? x[0] - y[0] : x[1] - y[1] });
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}
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Interval.merge = function(a, sorted)
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{
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if (typeof sorted == 'undefined') sorted = true;
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if (!sorted) Interval.sort(a);
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var k = 0;
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for (var i = 1; i < a.length; ++i) {
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if (a[k][1] >= a[i][0])
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a[k][1] = a[k][1] > a[i][1]? a[k][1] : a[i][1];
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else a[++k] = a[i].slice(0);
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}
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a.length = k + 1;
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}
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Interval.index_end = function(a, sorted)
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{
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if (a.length == 0) return;
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if (typeof sorted == 'undefined') sorted = true;
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if (!sorted) Interval.sort(a);
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a[0].push(0);
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var k = 0, k_en = a[0][1];
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for (var i = 1; i < a.length; ++i) {
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if (k_en <= a[i][0]) {
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for (++k; k < i; ++k)
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if (a[k][1] > a[i][0])
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break;
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k_en = a[k][1];
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}
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a[i].push(k);
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}
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}
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Interval.find_intv = function(a, x)
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{
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var left = -1, right = a.length;
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if (typeof a[0] == 'number') {
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while (right - left > 1) {
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var mid = left + ((right - left) >> 1);
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if (a[mid] > x) right = mid;
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else if (a[mid] < x) left = mid;
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else return mid;
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}
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} else {
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while (right - left > 1) {
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var mid = left + ((right - left) >> 1);
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if (a[mid][0] > x) right = mid;
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else if (a[mid][0] < x) left = mid;
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else return mid;
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}
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}
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return left;
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}
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Interval.find_ovlp = function(a, st, en)
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{
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if (a.length == 0 || st >= en) return [];
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var l = Interval.find_intv(a, st);
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var k = l < 0? 0 : a[l][a[l].length - 1];
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var b = [];
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for (var i = k; i < a.length; ++i) {
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if (a[i][0] >= en) break;
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else if (st < a[i][1])
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b.push(a[i]);
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}
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return b;
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}
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/*****************
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* Main function *
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*****************/
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function main(args)
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{
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var c, print_len = false;
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while ((c = getopt(args, "l")) != null) {
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if (c == 'l') print_len = true;
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}
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if (args.length - getopt.ind < 2) {
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print("Usage: k8 cnt-feat.js <target.bed> <feature.bed>");
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exit(1);
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}
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var file, buf = new Bytes();
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var target = {};
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file = new File(args[getopt.ind]);
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while (file.readline(buf) >= 0) {
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var t = buf.toString().split("\t");
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if (target[t[0]] == null)
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target[t[0]] = [];
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target[t[0]].push([parseInt(t[1]), parseInt(t[2]), 0, 0, 0]);
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}
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file.close();
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//warn('Read the target BED');
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for (var chr in target)
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Interval.index_end(target[chr], false);
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//warn('Indexed the target BED');
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var tot_len = 0, hit_len = 0;
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file = new File(args[getopt.ind+1]);
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while (file.readline(buf) >= 0) {
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var t = buf.toString().split("\t");
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var a = [];
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var bst = parseInt(t[1]);
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var ben = parseInt(t[2]);
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if (t.length >= 12 && /^\d+$/.test(t[9])) { // BED12
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t[9] = parseInt(t[9]);
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var sz = t[10].split(",");
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var st = t[11].split(",");
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for (var i = 0; i < t[9]; ++i) {
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st[i] = parseInt(st[i]);
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sz[i] = parseInt(sz[i]);
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a.push([bst + st[i], bst + st[i] + sz[i]]);
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}
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} else a.push([bst, ben]); // 3-column BED
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var feat_len = 0;
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for (var i = 0; i < a.length; ++i)
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feat_len += a[i][1] - a[i][0];
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tot_len += feat_len;
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if (target[t[0]] == null) continue;
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var b = [];
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for (var i = 0; i < a.length; ++i) {
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var o = Interval.find_ovlp(target[t[0]], a[i][0], a[i][1]);
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for (var j = 0; j < o.length; ++j) {
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var max_st = o[j][0] > a[i][0]? o[j][0] : a[i][0];
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var min_en = o[j][1] < a[i][1]? o[j][1] : a[i][1];
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b.push([max_st, min_en]);
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o[j][2] += min_en - max_st;
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++o[j][3];
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if (max_st == o[j][0] && min_en == o[j][1])
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++o[j][4];
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}
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}
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// find the length covered
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var feat_hit_len = 0;
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if (b.length > 0) {
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b.sort(function(a,b) {return a[0]-b[0]});
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var st = b[0][0], en = b[0][1];
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for (var i = 1; i < b.length; ++i) {
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if (b[i][0] <= en) en = en > b[i][1]? en : b[i][1];
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else feat_hit_len += en - st, st = b[i][0], en = b[i][1];
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}
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feat_hit_len += en - st;
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}
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hit_len += feat_hit_len;
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if (print_len) print(feat_len, feat_hit_len, buf);
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}
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file.close();
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buf.destroy();
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warn("# feature bases: " + tot_len);
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warn("# feature bases overlapping targets: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
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}
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main(arguments);
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