106 lines
3.5 KiB
JavaScript
106 lines
3.5 KiB
JavaScript
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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var c, min_ovlp = 2000, min_frac = 0.95, min_mapq = 10;
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while ((c = getopt(arguments, "q:l:f:")) != null) {
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if (c == 'q') min_mapq = parseInt(getopt.arg);
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else if (c == 'l') min_ovlp = parseInt(getopt.arg);
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else if (c == 'f') min_frac = parseFloat(getopt.arg);
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}
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if (arguments.length - getopt.ind < 2) {
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print("Usage: sort -k6,6 -k8,8n to-ref.paf | k8 ov-eval.js [options] - <ovlp.paf>");
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print("Options:");
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print(" -l INT min overlap length [2000]");
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print(" -q INT min mapping quality [10]");
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print(" -f FLOAT min fraction of mapped length [0.95]");
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exit(1);
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}
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var buf = new Bytes();
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var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
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var a = [], h = {};
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while (file.readline(buf) >= 0) {
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var t = buf.toString().split("\t");
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var is_pri = false;
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if (parseInt(t[11]) < min_mapq) continue;
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for (var i = 12; i < t.length; ++i)
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if (t[i] == 'tp:A:P')
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is_pri = true;
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if (!is_pri) continue;
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for (var i = 1; i <= 3; ++i)
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t[i] = parseInt(t[i]);
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for (var i = 6; i <= 8; ++i)
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t[i] = parseInt(t[i]);
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if (t[3] - t[2] < min_ovlp || t[8] - t[7] < min_ovlp || (t[3] - t[2]) / t[1] < min_frac)
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continue;
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var ctg = t[5], st = t[7], en = t[8];
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while (a.length > 0) {
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if (a[0][0] == ctg && a[0][2] > st)
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break;
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else a.shift();
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}
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for (var j = 0; j < a.length; ++j) {
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if (a[j][3] == t[0]) continue;
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var len = (en > a[j][2]? a[j][2] : en) - st;
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if (len >= min_ovlp) {
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var key = a[j][3] < t[0]? a[j][3] + "\t" + t[0] : t[0] + "\t" + a[j][3];
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h[key] = len;
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}
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}
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a.push([ctg, st, en, t[0]]);
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}
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file.close();
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file = new File(arguments[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 key = t[0] < t[5]? t[0] + "\t" + t[5] : t[5] + "\t" + t[0];
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if (h[key] > 0) h[key] = -h[key];
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}
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file.close();
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buf.destroy();
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var n_ovlp = 0, n_missing = 0;
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for (var key in h) {
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++n_ovlp;
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if (h[key] > 0) ++n_missing;
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}
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print(n_ovlp + " overlaps inferred from the reference mapping");
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print(n_missing + " missed by the read overlapper");
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print((100 * (1 - n_missing / n_ovlp)).toFixed(2) + "% sensitivity");
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