merging scripts into one long script
This commit is contained in:
Heng Li
parent
01560f1db0
commit
66c5e71fa8
107
misc/ov-eval.js
107
misc/ov-eval.js
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@ -1,107 +0,0 @@
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#!/usr/bin/env k8
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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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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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@ -0,0 +1,741 @@
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#!/usr/bin/env k8
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/*****************************
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***** Library functions *****
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*****************************/
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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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* Reverse and reverse complement *
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**********************************/
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Bytes.prototype.reverse = function()
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{
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for (var i = 0; i < this.length>>1; ++i) {
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var tmp = this[i];
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this[i] = this[this.length - i - 1];
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this[this.length - i - 1] = tmp;
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}
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}
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// reverse complement a DNA string
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Bytes.prototype.revcomp = function()
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{
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if (Bytes.rctab == null) {
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var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
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var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
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Bytes.rctab = [];
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for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
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for (var i = 0; i < s1.length; ++i)
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Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
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}
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for (var i = 0; i < this.length>>1; ++i) {
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var tmp = this[this.length - i - 1];
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this[this.length - i - 1] = Bytes.rctab[this[i]];
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this[i] = Bytes.rctab[tmp];
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}
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if (this.length&1)
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this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
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}
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/********************
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***** paftools *****
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********************/
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// variant calling
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function paf_call(args)
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{
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var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g;
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var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, min_mapq = 5;
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while ((c = getopt(args, "l:L:g:q:B:")) != null) {
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if (c == 'l') min_cov_len = parseInt(getopt.arg);
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else if (c == 'L') min_var_len = parseInt(getopt.arg);
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else if (c == 'g') gap_thres = parseInt(getopt.arg);
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else if (c == 'q') min_mapq = parseInt(getopt.arg);
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}
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if (args.length == getopt.ind) {
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print("Usage: sort -k6,6 -k8,8n <with-cs.paf> | paftools.js call [options] -");
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print("Options:");
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print(" -l INT min alignment length to compute coverage ["+min_cov_len+"]");
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print(" -L INT min alignment length to call variants ["+min_var_len+"]");
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print(" -q INT min mapping quality ["+min_mapq+"]");
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print(" -g INT short/long gap threshold (for statistics only) ["+gap_thres+"]");
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exit(1);
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}
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var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
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var buf = new Bytes();
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var tot_len = 0, n_sub = [0, 0, 0], n_ins = [0, 0, 0, 0], n_del = [0, 0, 0, 0];
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function count_var(o)
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{
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if (o[3] > 1) return;
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if (o[5] == '-' && o[6] == '-') return;
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if (o[5] == '-') { // insertion
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var l = o[6].length;
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if (l == 1) ++n_ins[0];
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else if (l == 2) ++n_ins[1];
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else if (l < gap_thres) ++n_ins[2];
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else ++n_ins[3];
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} else if (o[6] == '-') { // deletion
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var l = o[5].length;
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if (l == 1) ++n_del[0];
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else if (l == 2) ++n_del[1];
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else if (l < gap_thres) ++n_del[2];
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else ++n_del[3];
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} else {
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++n_sub[0];
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var s = o[5] + o[6];
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if (s == 'ag' || s == 'ga' || s == 'ct' || s == 'tc')
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++n_sub[1];
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else ++n_sub[2];
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}
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}
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var a = [], out = [];
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var c1_ctg = null, c1_start = 0, c1_end = 0, c1_counted = false, c1_len = 0;
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while (file.readline(buf) >= 0) {
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var line = buf.toString();
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if (!/\ts2:i:/.test(line)) continue; // skip secondary alignments
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var m, t = line.split("\t", 12);
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for (var i = 6; i <= 11; ++i)
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t[i] = parseInt(t[i]);
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if (t[10] < min_cov_len || t[11] < min_mapq) 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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var ctg = t[5], x = t[7], end = t[8];
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var query = t[0], rev = (t[4] == '-'), y = rev? t[3] : t[2];
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// compute regions covered by 1 contig
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if (ctg != c1_ctg || x >= c1_end) {
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if (c1_counted && c1_end > c1_start) {
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c1_len += c1_end - c1_start;
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print('R', c1_ctg, c1_start, c1_end);
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}
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c1_ctg = ctg, c1_start = x, c1_end = end;
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c1_counted = (t[10] >= min_var_len);
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} else if (end > c1_end) { // overlap
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if (c1_counted && x > c1_start) {
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c1_len += x - c1_start;
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print('R', c1_ctg, c1_start, x);
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}
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c1_start = c1_end, c1_end = end;
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c1_counted = (t[10] >= min_var_len);
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} else { // contained
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if (c1_counted && x > c1_start) {
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c1_len += x - c1_start;
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print('R', c1_ctg, c1_start, x);
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}
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c1_start = end;
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}
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// output variants ahead of this alignment
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while (out.length) {
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if (out[0][0] != ctg || out[0][2] <= x) {
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count_var(out[0]);
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print('V', out[0].join("\t"));
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out.shift();
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} else break;
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}
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// update coverage
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for (var i = 0; i < out.length; ++i)
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if (out[i][1] >= x && out[i][2] <= end)
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++out[i][3];
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// drop alignments that don't overlap with the current one
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var k = 0;
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for (var i = 0; i < a.length; ++i)
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if (a[0][0] == ctg && a[0][2] > x)
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a[k++] = a[i];
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a.length = k;
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// core loop
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if (t[10] >= min_var_len) {
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if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue; // no cs tag
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var cs = m[1];
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var blen = 0, n_diff = 0;
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tot_len += t[10];
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while ((m = re_cs.exec(cs)) != null) {
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var cov = 1;
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if (m[1] == '*' || m[1] == '+' || m[1] == '-')
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for (var i = 0; i < a.length; ++i)
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if (a[0][2] > x) ++cov;
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var qs, qe;
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if (m[1] == '=' || m[1] == ':') {
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var l = m[1] == '='? m[2].length : parseInt(m[2]);
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if (rev) y -= l;
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else y += l;
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x += l, blen += l;
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} else if (m[1] == '*') {
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if (rev) qs = y - 1, qe = y, --y;
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else qs = y, qe = y + 1, ++y;
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out.push([t[5], x, x+1, cov, t[11], m[2].charAt(0), m[2].charAt(1), query, qs, qe, rev? '-' : '+']);
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++x, ++blen, ++n_diff;
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} else if (m[1] == '+') {
|
||||
var l = m[2].length;
|
||||
if (rev) qs = y - l, qe = y, y -= l;
|
||||
else qs = y, qe = y + l, y += l;
|
||||
out.push([t[5], x, x, cov, t[11], '-', m[2], query, qs, qe, rev? '-' : '+']);
|
||||
++blen, ++n_diff;
|
||||
} else if (m[1] == '-') {
|
||||
var l = m[2].length;
|
||||
out.push([t[5], x, x + l, cov, t[11], m[2], '-', query, y, y, rev? '-' : '+']);
|
||||
x += l, ++blen, ++n_diff;
|
||||
}
|
||||
}
|
||||
}
|
||||
a.push([t[5], t[7], t[8]]);
|
||||
}
|
||||
if (c1_counted && c1_end > c1_start) {
|
||||
c1_len += c1_end - c1_start;
|
||||
print('R', c1_ctg, c1_start, c1_end);
|
||||
}
|
||||
while (out.length) {
|
||||
count_var(out[0]);
|
||||
print('V', out[0].join("\t"));
|
||||
out.shift();
|
||||
}
|
||||
|
||||
//warn(tot_len + " alignment columns considered in calling");
|
||||
warn(c1_len + " reference bases covered by exactly one contig");
|
||||
warn(n_sub[0] + " substitutions; ts/tv = " + (n_sub[1]/n_sub[2]).toFixed(3));
|
||||
warn(n_del[0] + " 1bp deletions");
|
||||
warn(n_ins[0] + " 1bp insertions");
|
||||
warn(n_del[1] + " 2bp deletions");
|
||||
warn(n_ins[1] + " 2bp insertions");
|
||||
warn(n_del[2] + " [3,"+gap_thres+") deletions");
|
||||
warn(n_ins[2] + " [3,"+gap_thres+") insertions");
|
||||
warn(n_del[3] + " >="+gap_thres+" deletions");
|
||||
warn(n_ins[3] + " >="+gap_thres+" insertions");
|
||||
|
||||
buf.destroy();
|
||||
file.close();
|
||||
}
|
||||
|
||||
/**************************
|
||||
*** Evaluation related ***
|
||||
**************************/
|
||||
|
||||
// evaluate mapping accuracy
|
||||
function paf_mapeval(args)
|
||||
{
|
||||
var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.1, cap_short_mapq = false;
|
||||
while ((c = getopt(args, "Q:r:m:c")) != null) {
|
||||
if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
|
||||
else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
|
||||
else if (c == 'm') mode = parseInt(getopt.arg);
|
||||
else if (c == 'c') cap_short_mapq = true;
|
||||
}
|
||||
|
||||
if (args.length == getopt.ind) {
|
||||
warn("Usage: paftools.js mapeval [options] <in.paf>|<in.sam>");
|
||||
warn("Options:");
|
||||
warn(" -r FLOAT mapping correct if overlap_length/union_length>FLOAT [" + ovlp_ratio + "]");
|
||||
warn(" -Q INT print wrong mappings with mapQ>INT [don't print]");
|
||||
warn(" -m INT 0: eval the longest aln only; 1: first aln only; 2: all primary aln [0]");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
|
||||
var buf = new Bytes();
|
||||
|
||||
var tot = [], err = [];
|
||||
for (var q = 0; q <= max_mapq; ++q)
|
||||
tot[q] = err[q] = 0;
|
||||
|
||||
function is_correct(s, b)
|
||||
{
|
||||
if (s[0] != b[0] || s[3] != b[3]) return false;
|
||||
var o, l;
|
||||
if (s[1] < b[1]) {
|
||||
if (s[2] <= b[1]) return false;
|
||||
o = (s[2] < b[2]? s[2] : b[2]) - b[1];
|
||||
l = (s[2] > b[2]? s[2] : b[2]) - s[1];
|
||||
} else {
|
||||
if (b[2] <= s[1]) return false;
|
||||
o = (s[2] < b[2]? s[2] : b[2]) - s[1];
|
||||
l = (s[2] > b[2]? s[2] : b[2]) - b[1];
|
||||
}
|
||||
return o/l > ovlp_ratio? true : false;
|
||||
}
|
||||
|
||||
function count_err(qname, a, tot, err, mode)
|
||||
{
|
||||
if (a.length == 0) return;
|
||||
|
||||
var m, s;
|
||||
if ((m = /^(\S+)!(\S+)!(\d+)!(\d+)!([\+\-])$/.exec(qname)) != null) { // pbsim single-end reads
|
||||
s = [m[1], m[2], parseInt(m[3]), parseInt(m[4]), m[5]];
|
||||
} else if ((m = /^(\S+)!(\S+)!(\d+)_(\d+)!(\d+)_(\d+)!([\+\-])([\+\-])\/([12])$/.exec(qname)) != null) { // mason2 paired-end reads
|
||||
if (m[9] == '1') {
|
||||
s = [m[1], m[2], parseInt(m[3]), parseInt(m[5]), m[7]];
|
||||
} else {
|
||||
s = [m[1], m[2], parseInt(m[4]), parseInt(m[6]), m[8]];
|
||||
}
|
||||
} else throw Error("Failed to parse simulated read names '" + qname + "'");
|
||||
s.shift(); // skip the orginal read name
|
||||
|
||||
if (mode == 0 || mode == 1) { // longest only or first only
|
||||
var max_i = 0;
|
||||
if (mode == 0) { // longest only
|
||||
var max = 0;
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][5] > max)
|
||||
max = a[i][5], max_i = i;
|
||||
}
|
||||
var mapq = a[max_i][4];
|
||||
++tot[mapq];
|
||||
if (!is_correct(s, a[max_i])) {
|
||||
if (mapq >= err_out_q)
|
||||
print('E', qname, a[max_i].join("\t"));
|
||||
++err[mapq];
|
||||
}
|
||||
} else if (mode == 2) { // all primary mode
|
||||
var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
|
||||
if (cap_short_mapq) {
|
||||
var max = 0, max_q = 0;
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][5] > max)
|
||||
max = a[i][5], max_q = a[i][4];
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
a[i][4] = max_q < a[i][4]? max_q : a[i][4];
|
||||
}
|
||||
for (var i = 0; i < a.length; ++i) {
|
||||
max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
|
||||
if (!is_correct(s, a[i]))
|
||||
if (a[i][4] > max_err_mapq)
|
||||
max_err_mapq = a[i][4], max_err_i = i;
|
||||
}
|
||||
if (max_err_mapq >= 0) {
|
||||
++tot[max_err_mapq], ++err[max_err_mapq];
|
||||
if (max_err_mapq >= err_out_q)
|
||||
print('E', qname, a[max_err_i].join("\t"));
|
||||
} else ++tot[max_mapq];
|
||||
}
|
||||
}
|
||||
|
||||
var lineno = 0, last = null, a = [], n_unmapped = null;
|
||||
var re_cigar = /(\d+)([MIDSHN])/g;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var m, line = buf.toString();
|
||||
++lineno;
|
||||
if (line[0] != '@') {
|
||||
var t = line.split("\t");
|
||||
if (t[4] == '+' || t[4] == '-') { // PAF
|
||||
if (last != t[0]) {
|
||||
if (last != null) count_err(last, a, tot, err, mode);
|
||||
a = [], last = t[0];
|
||||
}
|
||||
if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
|
||||
continue;
|
||||
var mapq = parseInt(t[11]);
|
||||
if (mapq > max_mapq) mapq = max_mapq;
|
||||
a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
|
||||
} else { // SAM
|
||||
var flag = parseInt(t[1]);
|
||||
var read_no = flag>>6&0x3;
|
||||
var qname = t[0];
|
||||
if (!/\/[12]$/.test(qname))
|
||||
qname = read_no == 1 || read_no == 2? t[0] + '/' + read_no : t[0];
|
||||
if (last != qname) {
|
||||
if (last != null) count_err(last, a, tot, err, mode);
|
||||
a = [], last = qname;
|
||||
}
|
||||
if (flag&0x100) continue; // secondary alignment
|
||||
if ((flag&0x4) || t[2] == '*') { // unmapped
|
||||
if (n_unmapped == null) n_unmapped = 0;
|
||||
++n_unmapped;
|
||||
continue;
|
||||
}
|
||||
var mapq = parseInt(t[4]);
|
||||
if (mapq > max_mapq) mapq = max_mapq;
|
||||
var pos = parseInt(t[3]) - 1, pos_end = pos;
|
||||
var n_gap = 0, mlen = 0;
|
||||
while ((m = re_cigar.exec(t[5])) != null) {
|
||||
var len = parseInt(m[1]);
|
||||
if (m[2] == 'M') pos_end += len, mlen += len;
|
||||
else if (m[2] == 'I') n_gap += len;
|
||||
else if (m[2] == 'D') n_gap += len, pos_end += len;
|
||||
}
|
||||
var score = pos_end - pos;
|
||||
if ((m = /\tNM:i:(\d+)/.exec(line)) != null) {
|
||||
var NM = parseInt(m[1]);
|
||||
if (NM >= n_gap) score = mlen - (NM - n_gap);
|
||||
}
|
||||
a.push([t[2], pos, pos_end, (flag&16)? '-' : '+', mapq, score]);
|
||||
}
|
||||
}
|
||||
}
|
||||
if (last != null) count_err(last, a, tot, err, mode);
|
||||
|
||||
buf.destroy();
|
||||
file.close();
|
||||
|
||||
var sum_tot = 0, sum_err = 0, q_out = -1, sum_tot2 = 0, sum_err2 = 0;
|
||||
for (var q = max_mapq; q >= 0; --q) {
|
||||
if (tot[q] == 0) continue;
|
||||
if (q_out < 0 || err[q] > 0) {
|
||||
if (q_out >= 0) print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
|
||||
sum_tot = sum_err = 0, q_out = q;
|
||||
}
|
||||
sum_tot += tot[q], sum_err += err[q];
|
||||
sum_tot2 += tot[q], sum_err2 += err[q];
|
||||
}
|
||||
print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
|
||||
if (n_unmapped != null) print('U', n_unmapped);
|
||||
}
|
||||
|
||||
// convert mason2 SAM to FASTQ
|
||||
function paf_mason2fq(args)
|
||||
{
|
||||
if (args.length == 0) {
|
||||
print("Usage: paftools.js mason2fq <mason.sam>");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
function print_se(a)
|
||||
{
|
||||
print('@' + a.slice(0, 5).join("!") + " " + a[8]);
|
||||
print(a[5]);
|
||||
print("+");
|
||||
print(a[6]);
|
||||
}
|
||||
|
||||
var buf = new Bytes(), buf2 = new Bytes();
|
||||
var file = new File(args[0]);
|
||||
var re = /(\d+)([MIDSHN])/g;
|
||||
var last = null;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
if (t[0].charAt(0) == '@') continue;
|
||||
var m, l_ref = 0;
|
||||
while ((m = re.exec(t[5])) != null)
|
||||
if (m[2] == 'D' || m[2] == 'M' || m[2] == 'N')
|
||||
l_ref += parseInt(m[1]);
|
||||
var flag = parseInt(t[1]);
|
||||
var rev = !!(flag&16);
|
||||
var seq, qual;
|
||||
if (rev) {
|
||||
buf2.length = 0;
|
||||
buf2.set(t[9], 0);
|
||||
buf2.revcomp();
|
||||
seq = buf2.toString();
|
||||
buf2.set(t[10], 0);
|
||||
buf2.reverse();
|
||||
qual = buf2.toString();
|
||||
} else seq = t[9], qual = t[10];
|
||||
var qname = t[0];
|
||||
qname = qname.replace(/^simulated./, "");
|
||||
var chr = t[2];
|
||||
var pos = parseInt(t[3]) - 1;
|
||||
var strand = (flag&16)? '-' : '+';
|
||||
var read_no = flag&0xc0;
|
||||
if (read_no == 0x40) read_no = 1;
|
||||
else if (read_no == 0x80) read_no = 2;
|
||||
else read_no = 0;
|
||||
var err = 0, snp = 0, indel = 0;
|
||||
for (var i = 11; i < t.length; ++i) {
|
||||
if ((m = /^XE:i:(\d+)/.exec(t[i])) != null) err = m[1];
|
||||
else if ((m = /^XS:i:(\d+)/.exec(t[i])) != null) snp = m[1];
|
||||
else if ((m = /^XI:i:(\d+)/.exec(t[i])) != null) indel = m[1];
|
||||
}
|
||||
var comment = [err, snp, indel].join(":");
|
||||
if (last == null) {
|
||||
last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
|
||||
} else if (last[0] != qname) {
|
||||
print_se(last);
|
||||
last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
|
||||
} else {
|
||||
if (read_no == 2) { // last[] is the first read
|
||||
if (last[7] != 1) throw Error("ERROR: can't find read1");
|
||||
var name = [qname, chr, last[2] + "_" + pos, last[3] + "_" + (pos + l_ref), last[4] + strand].join("!");
|
||||
print('@' + name + '/1' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
|
||||
print('@' + name + '/2' + ' ' + comment); print(seq); print("+"); print(qual);
|
||||
} else {
|
||||
if (last[7] != 2) throw Error("ERROR: can't find read2");
|
||||
var name = [qname, chr, pos + "_" + last[2], (pos + l_ref) + "_" + last[3], strand + last[4]].join("!");
|
||||
print('@' + name + '/1' + ' ' + comment); print(seq); print("+"); print(qual);
|
||||
print('@' + name + '/2' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
|
||||
}
|
||||
last = null;
|
||||
}
|
||||
}
|
||||
if (last != null) print_se(last);
|
||||
file.close();
|
||||
buf.destroy();
|
||||
buf2.destroy();
|
||||
}
|
||||
|
||||
// convert pbsim MAF to FASTQ
|
||||
function paf_pbsim2fq(args)
|
||||
{
|
||||
if (args.length < 2) {
|
||||
print("Usage: paftools.js pbsim2fq <ref.fa.fai> <pbsim1.maf> [[pbsim2.maf] ...]");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var file, buf = new Bytes(), buf2 = new Bytes();
|
||||
file = new File(args[0]);
|
||||
var chr_list = [];
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split(/\s+/);
|
||||
chr_list.push(t[0]);
|
||||
}
|
||||
file.close();
|
||||
|
||||
for (var k = 1; k < args.length; ++k) {
|
||||
var fn = args[k];
|
||||
file = new File(fn);
|
||||
var state = 0, reg;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var line = buf.toString();
|
||||
if (state == 0 && line.charAt(0) == 'a') {
|
||||
state = 1;
|
||||
} else if (state == 1 && line.charAt(0) == 's') {
|
||||
var t = line.split(/\s+/);
|
||||
var st = parseInt(t[2]);
|
||||
reg = [st, st + parseInt(t[3])];
|
||||
state = 2;
|
||||
} else if (state == 2 && line.charAt(0) == 's') {
|
||||
var m, t = line.split(/\s+/);
|
||||
if ((m = /S(\d+)_\d+/.exec(t[1])) == null) throw Error("Failed to parse the read name");
|
||||
var chr_id = parseInt(m[1]) - 1;
|
||||
if (chr_id >= chr_list.length) throw Error("Index outside the chr list");
|
||||
var name = [t[1], chr_list[chr_id], reg[0], reg[1], t[4]].join("!");
|
||||
var seq = t[6].replace(/\-/g, "");
|
||||
if (seq.length != parseInt(t[5])) throw Error("Inconsistent read length");
|
||||
if (seq.indexOf("NN") < 0) {
|
||||
if (t[4] == '-') {
|
||||
buf2.set(seq, 0);
|
||||
buf2.length = seq.length;
|
||||
buf2.revcomp();
|
||||
seq = buf2.toString();
|
||||
}
|
||||
print(">" + name);
|
||||
print(seq);
|
||||
}
|
||||
state = 0;
|
||||
}
|
||||
}
|
||||
file.close();
|
||||
}
|
||||
buf.destroy();
|
||||
buf2.destroy();
|
||||
}
|
||||
|
||||
function paf_ov_eval(args)
|
||||
{
|
||||
var c, min_ovlp = 2000, min_frac = 0.95, min_mapq = 10;
|
||||
while ((c = getopt(args, "q:l:f:")) != null) {
|
||||
if (c == 'q') min_mapq = parseInt(getopt.arg);
|
||||
else if (c == 'l') min_ovlp = parseInt(getopt.arg);
|
||||
else if (c == 'f') min_frac = parseFloat(getopt.arg);
|
||||
}
|
||||
if (args.length - getopt.ind < 2) {
|
||||
print("Usage: sort -k6,6 -k8,8n to-ref.paf | paftools.js ov-eval [options] - <ovlp.paf>");
|
||||
print("Options:");
|
||||
print(" -l INT min overlap length [2000]");
|
||||
print(" -q INT min mapping quality [10]");
|
||||
print(" -f FLOAT min fraction of mapped length [0.95]");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var buf = new Bytes();
|
||||
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
|
||||
var a = [], h = {};
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
var is_pri = false;
|
||||
if (parseInt(t[11]) < min_mapq) continue;
|
||||
for (var i = 12; i < t.length; ++i)
|
||||
if (t[i] == 'tp:A:P')
|
||||
is_pri = true;
|
||||
if (!is_pri) continue;
|
||||
for (var i = 1; i <= 3; ++i)
|
||||
t[i] = parseInt(t[i]);
|
||||
for (var i = 6; i <= 8; ++i)
|
||||
t[i] = parseInt(t[i]);
|
||||
if (t[3] - t[2] < min_ovlp || t[8] - t[7] < min_ovlp || (t[3] - t[2]) / t[1] < min_frac)
|
||||
continue;
|
||||
var ctg = t[5], st = t[7], en = t[8];
|
||||
while (a.length > 0) {
|
||||
if (a[0][0] == ctg && a[0][2] > st)
|
||||
break;
|
||||
else a.shift();
|
||||
}
|
||||
for (var j = 0; j < a.length; ++j) {
|
||||
if (a[j][3] == t[0]) continue;
|
||||
var len = (en > a[j][2]? a[j][2] : en) - st;
|
||||
if (len >= min_ovlp) {
|
||||
var key = a[j][3] < t[0]? a[j][3] + "\t" + t[0] : t[0] + "\t" + a[j][3];
|
||||
h[key] = len;
|
||||
}
|
||||
}
|
||||
a.push([ctg, st, en, t[0]]);
|
||||
}
|
||||
file.close();
|
||||
|
||||
file = new File(args[getopt.ind + 1]);
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
var key = t[0] < t[5]? t[0] + "\t" + t[5] : t[5] + "\t" + t[0];
|
||||
if (h[key] > 0) h[key] = -h[key];
|
||||
}
|
||||
file.close();
|
||||
buf.destroy();
|
||||
|
||||
var n_ovlp = 0, n_missing = 0;
|
||||
for (var key in h) {
|
||||
++n_ovlp;
|
||||
if (h[key] > 0) ++n_missing;
|
||||
}
|
||||
print(n_ovlp + " overlaps inferred from the reference mapping");
|
||||
print(n_missing + " missed by the read overlapper");
|
||||
print((100 * (1 - n_missing / n_ovlp)).toFixed(2) + "% sensitivity");
|
||||
}
|
||||
|
||||
/*************************
|
||||
***** main function *****
|
||||
*************************/
|
||||
|
||||
function main(args)
|
||||
{
|
||||
if (args.length == 0) {
|
||||
print("Usage: paftools.js <command> [arguments]");
|
||||
print("Commands:");
|
||||
print(" call call variants from asm-to-ref alignment with the cs tag");
|
||||
print("");
|
||||
print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
|
||||
print(" mason2fq convert mason2-simulated SAM to FASTQ");
|
||||
print(" pbsim2fq convert PBSIM-simulated MAF to FASTQ");
|
||||
print(" ov-eval evaluate read overlap sensitivity using read-to-ref mapping");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var cmd = args.shift();
|
||||
if (cmd == 'call') paf_call(args);
|
||||
else if (cmd == 'mapeval') paf_mapeval(args);
|
||||
else if (cmd == 'mason2fq') paf_mason2fq(args);
|
||||
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
|
||||
else if (cmd == 'ov-eval') paf_ov_eval(args);
|
||||
else throw Error("unrecognized command: " + cmd);
|
||||
}
|
||||
|
||||
main(arguments);
|
||||
204
misc/sim-eval.js
204
misc/sim-eval.js
|
|
@ -1,204 +0,0 @@
|
|||
#!/usr/bin/env k8
|
||||
|
||||
var getopt = function(args, ostr) {
|
||||
var oli; // option letter list index
|
||||
if (typeof(getopt.place) == 'undefined')
|
||||
getopt.ind = 0, getopt.arg = null, getopt.place = -1;
|
||||
if (getopt.place == -1) { // update scanning pointer
|
||||
if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
|
||||
getopt.place = -1;
|
||||
return null;
|
||||
}
|
||||
if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
|
||||
++getopt.ind;
|
||||
getopt.place = -1;
|
||||
return null;
|
||||
}
|
||||
}
|
||||
var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
|
||||
if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
|
||||
if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
|
||||
if (getopt.place < 0) ++getopt.ind;
|
||||
return '?';
|
||||
}
|
||||
if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
|
||||
getopt.arg = null;
|
||||
if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
|
||||
} else { // need an argument
|
||||
if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
|
||||
getopt.arg = args[getopt.ind].substr(getopt.place);
|
||||
else if (args.length <= ++getopt.ind) { // no arg
|
||||
getopt.place = -1;
|
||||
if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
|
||||
return '?';
|
||||
} else getopt.arg = args[getopt.ind]; // white space
|
||||
getopt.place = -1;
|
||||
++getopt.ind;
|
||||
}
|
||||
return optopt;
|
||||
}
|
||||
|
||||
var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.1, cap_short_mapq = false;
|
||||
while ((c = getopt(arguments, "Q:r:m:c")) != null) {
|
||||
if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
|
||||
else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
|
||||
else if (c == 'm') mode = parseInt(getopt.arg);
|
||||
else if (c == 'c') cap_short_mapq = true;
|
||||
}
|
||||
|
||||
if (arguments.length == getopt.ind) {
|
||||
warn("Usage: k8 sim-eval.js [options] <in.paf>|<in.sam>");
|
||||
warn("Options:");
|
||||
warn(" -r FLOAT mapping correct if overlap_length/union_length>FLOAT [" + ovlp_ratio + "]");
|
||||
warn(" -Q INT print wrong mappings with mapQ>INT [don't print]");
|
||||
warn(" -m INT 0: eval the longest aln only; 1: first aln only; 2: all primary aln [0]");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
|
||||
var buf = new Bytes();
|
||||
|
||||
var tot = [], err = [];
|
||||
for (var q = 0; q <= max_mapq; ++q)
|
||||
tot[q] = err[q] = 0;
|
||||
|
||||
function is_correct(s, b)
|
||||
{
|
||||
if (s[0] != b[0] || s[3] != b[3]) return false;
|
||||
var o, l;
|
||||
if (s[1] < b[1]) {
|
||||
if (s[2] <= b[1]) return false;
|
||||
o = (s[2] < b[2]? s[2] : b[2]) - b[1];
|
||||
l = (s[2] > b[2]? s[2] : b[2]) - s[1];
|
||||
} else {
|
||||
if (b[2] <= s[1]) return false;
|
||||
o = (s[2] < b[2]? s[2] : b[2]) - s[1];
|
||||
l = (s[2] > b[2]? s[2] : b[2]) - b[1];
|
||||
}
|
||||
return o/l > ovlp_ratio? true : false;
|
||||
}
|
||||
|
||||
function count_err(qname, a, tot, err, mode)
|
||||
{
|
||||
if (a.length == 0) return;
|
||||
|
||||
var m, s;
|
||||
if ((m = /^(\S+)!(\S+)!(\d+)!(\d+)!([\+\-])$/.exec(qname)) != null) { // pbsim single-end reads
|
||||
s = [m[1], m[2], parseInt(m[3]), parseInt(m[4]), m[5]];
|
||||
} else if ((m = /^(\S+)!(\S+)!(\d+)_(\d+)!(\d+)_(\d+)!([\+\-])([\+\-])\/([12])$/.exec(qname)) != null) { // mason2 paired-end reads
|
||||
if (m[9] == '1') {
|
||||
s = [m[1], m[2], parseInt(m[3]), parseInt(m[5]), m[7]];
|
||||
} else {
|
||||
s = [m[1], m[2], parseInt(m[4]), parseInt(m[6]), m[8]];
|
||||
}
|
||||
} else throw Error("Failed to parse simulated read names '" + qname + "'");
|
||||
s.shift(); // skip the orginal read name
|
||||
|
||||
if (mode == 0 || mode == 1) { // longest only or first only
|
||||
var max_i = 0;
|
||||
if (mode == 0) { // longest only
|
||||
var max = 0;
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][5] > max)
|
||||
max = a[i][5], max_i = i;
|
||||
}
|
||||
var mapq = a[max_i][4];
|
||||
++tot[mapq];
|
||||
if (!is_correct(s, a[max_i])) {
|
||||
if (mapq >= err_out_q)
|
||||
print('E', qname, a[max_i].join("\t"));
|
||||
++err[mapq];
|
||||
}
|
||||
} else if (mode == 2) { // all primary mode
|
||||
var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
|
||||
if (cap_short_mapq) {
|
||||
var max = 0, max_q = 0;
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
if (a[i][5] > max)
|
||||
max = a[i][5], max_q = a[i][4];
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
a[i][4] = max_q < a[i][4]? max_q : a[i][4];
|
||||
}
|
||||
for (var i = 0; i < a.length; ++i) {
|
||||
max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
|
||||
if (!is_correct(s, a[i]))
|
||||
if (a[i][4] > max_err_mapq)
|
||||
max_err_mapq = a[i][4], max_err_i = i;
|
||||
}
|
||||
if (max_err_mapq >= 0) {
|
||||
++tot[max_err_mapq], ++err[max_err_mapq];
|
||||
if (max_err_mapq >= err_out_q)
|
||||
print('E', qname, a[max_err_i].join("\t"));
|
||||
} else ++tot[max_mapq];
|
||||
}
|
||||
}
|
||||
|
||||
var lineno = 0, last = null, a = [], n_unmapped = null;
|
||||
var re_cigar = /(\d+)([MIDSHN])/g;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var m, line = buf.toString();
|
||||
++lineno;
|
||||
if (line[0] != '@') {
|
||||
var t = line.split("\t");
|
||||
if (t[4] == '+' || t[4] == '-') { // PAF
|
||||
if (last != t[0]) {
|
||||
if (last != null) count_err(last, a, tot, err, mode);
|
||||
a = [], last = t[0];
|
||||
}
|
||||
if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
|
||||
continue;
|
||||
var mapq = parseInt(t[11]);
|
||||
if (mapq > max_mapq) mapq = max_mapq;
|
||||
a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
|
||||
} else { // SAM
|
||||
var flag = parseInt(t[1]);
|
||||
var read_no = flag>>6&0x3;
|
||||
var qname = t[0];
|
||||
if (!/\/[12]$/.test(qname))
|
||||
qname = read_no == 1 || read_no == 2? t[0] + '/' + read_no : t[0];
|
||||
if (last != qname) {
|
||||
if (last != null) count_err(last, a, tot, err, mode);
|
||||
a = [], last = qname;
|
||||
}
|
||||
if (flag&0x100) continue; // secondary alignment
|
||||
if ((flag&0x4) || t[2] == '*') { // unmapped
|
||||
if (n_unmapped == null) n_unmapped = 0;
|
||||
++n_unmapped;
|
||||
continue;
|
||||
}
|
||||
var mapq = parseInt(t[4]);
|
||||
if (mapq > max_mapq) mapq = max_mapq;
|
||||
var pos = parseInt(t[3]) - 1, pos_end = pos;
|
||||
var n_gap = 0, mlen = 0;
|
||||
while ((m = re_cigar.exec(t[5])) != null) {
|
||||
var len = parseInt(m[1]);
|
||||
if (m[2] == 'M') pos_end += len, mlen += len;
|
||||
else if (m[2] == 'I') n_gap += len;
|
||||
else if (m[2] == 'D') n_gap += len, pos_end += len;
|
||||
}
|
||||
var score = pos_end - pos;
|
||||
if ((m = /\tNM:i:(\d+)/.exec(line)) != null) {
|
||||
var NM = parseInt(m[1]);
|
||||
if (NM >= n_gap) score = mlen - (NM - n_gap);
|
||||
}
|
||||
a.push([t[2], pos, pos_end, (flag&16)? '-' : '+', mapq, score]);
|
||||
}
|
||||
}
|
||||
}
|
||||
if (last != null) count_err(last, a, tot, err, mode);
|
||||
|
||||
buf.destroy();
|
||||
file.close();
|
||||
|
||||
var sum_tot = 0, sum_err = 0, q_out = -1, sum_tot2 = 0, sum_err2 = 0;
|
||||
for (var q = max_mapq; q >= 0; --q) {
|
||||
if (tot[q] == 0) continue;
|
||||
if (q_out < 0 || err[q] > 0) {
|
||||
if (q_out >= 0) print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
|
||||
sum_tot = sum_err = 0, q_out = q;
|
||||
}
|
||||
sum_tot += tot[q], sum_err += err[q];
|
||||
sum_tot2 += tot[q], sum_err2 += err[q];
|
||||
}
|
||||
print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
|
||||
if (n_unmapped != null) print('U', n_unmapped);
|
||||
|
|
@ -1,107 +0,0 @@
|
|||
#!/usr/bin/env k8
|
||||
|
||||
Bytes.prototype.reverse = function()
|
||||
{
|
||||
for (var i = 0; i < this.length>>1; ++i) {
|
||||
var tmp = this[i];
|
||||
this[i] = this[this.length - i - 1];
|
||||
this[this.length - i - 1] = tmp;
|
||||
}
|
||||
}
|
||||
|
||||
// reverse complement a DNA string
|
||||
Bytes.prototype.revcomp = function()
|
||||
{
|
||||
if (Bytes.rctab == null) {
|
||||
var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
|
||||
var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
|
||||
Bytes.rctab = [];
|
||||
for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
|
||||
for (var i = 0; i < s1.length; ++i)
|
||||
Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
|
||||
}
|
||||
for (var i = 0; i < this.length>>1; ++i) {
|
||||
var tmp = this[this.length - i - 1];
|
||||
this[this.length - i - 1] = Bytes.rctab[this[i]];
|
||||
this[i] = Bytes.rctab[tmp];
|
||||
}
|
||||
if (this.length&1)
|
||||
this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
|
||||
}
|
||||
|
||||
if (arguments.length == 0) {
|
||||
print("Usage: k8 sim-mason2.js <mason.sam>");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
function print_se(a)
|
||||
{
|
||||
print('@' + a.slice(0, 5).join("!") + " " + a[8]);
|
||||
print(a[5]);
|
||||
print("+");
|
||||
print(a[6]);
|
||||
}
|
||||
|
||||
var buf = new Bytes(), buf2 = new Bytes();
|
||||
var file = new File(arguments[0]);
|
||||
var re = /(\d+)([MIDSHN])/g;
|
||||
var last = null;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
if (t[0].charAt(0) == '@') continue;
|
||||
var m, l_ref = 0;
|
||||
while ((m = re.exec(t[5])) != null)
|
||||
if (m[2] == 'D' || m[2] == 'M' || m[2] == 'N')
|
||||
l_ref += parseInt(m[1]);
|
||||
var flag = parseInt(t[1]);
|
||||
var rev = !!(flag&16);
|
||||
var seq, qual;
|
||||
if (rev) {
|
||||
buf2.length = 0;
|
||||
buf2.set(t[9], 0);
|
||||
buf2.revcomp();
|
||||
seq = buf2.toString();
|
||||
buf2.set(t[10], 0);
|
||||
buf2.reverse();
|
||||
qual = buf2.toString();
|
||||
} else seq = t[9], qual = t[10];
|
||||
var qname = t[0];
|
||||
qname = qname.replace(/^simulated./, "");
|
||||
var chr = t[2];
|
||||
var pos = parseInt(t[3]) - 1;
|
||||
var strand = (flag&16)? '-' : '+';
|
||||
var read_no = flag&0xc0;
|
||||
if (read_no == 0x40) read_no = 1;
|
||||
else if (read_no == 0x80) read_no = 2;
|
||||
else read_no = 0;
|
||||
var err = 0, snp = 0, indel = 0;
|
||||
for (var i = 11; i < t.length; ++i) {
|
||||
if ((m = /^XE:i:(\d+)/.exec(t[i])) != null) err = m[1];
|
||||
else if ((m = /^XS:i:(\d+)/.exec(t[i])) != null) snp = m[1];
|
||||
else if ((m = /^XI:i:(\d+)/.exec(t[i])) != null) indel = m[1];
|
||||
}
|
||||
var comment = [err, snp, indel].join(":");
|
||||
if (last == null) {
|
||||
last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
|
||||
} else if (last[0] != qname) {
|
||||
print_se(last);
|
||||
last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
|
||||
} else {
|
||||
if (read_no == 2) { // last[] is the first read
|
||||
if (last[7] != 1) throw Error("ERROR: can't find read1");
|
||||
var name = [qname, chr, last[2] + "_" + pos, last[3] + "_" + (pos + l_ref), last[4] + strand].join("!");
|
||||
print('@' + name + '/1' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
|
||||
print('@' + name + '/2' + ' ' + comment); print(seq); print("+"); print(qual);
|
||||
} else {
|
||||
if (last[7] != 2) throw Error("ERROR: can't find read2");
|
||||
var name = [qname, chr, pos + "_" + last[2], (pos + l_ref) + "_" + last[3], strand + last[4]].join("!");
|
||||
print('@' + name + '/1' + ' ' + comment); print(seq); print("+"); print(qual);
|
||||
print('@' + name + '/2' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
|
||||
}
|
||||
last = null;
|
||||
}
|
||||
}
|
||||
if (last != null) print_se(last);
|
||||
file.close();
|
||||
buf.destroy();
|
||||
buf2.destroy();
|
||||
|
|
@ -1,83 +0,0 @@
|
|||
#!/usr/bin/env k8
|
||||
|
||||
Bytes.prototype.reverse = function()
|
||||
{
|
||||
for (var i = 0; i < this.length>>1; ++i) {
|
||||
var tmp = this[i];
|
||||
this[i] = this[this.length - i - 1];
|
||||
this[this.length - i - 1] = tmp;
|
||||
}
|
||||
}
|
||||
|
||||
// reverse complement a DNA string
|
||||
Bytes.prototype.revcomp = function()
|
||||
{
|
||||
if (Bytes.rctab == null) {
|
||||
var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
|
||||
var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
|
||||
Bytes.rctab = [];
|
||||
for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
|
||||
for (var i = 0; i < s1.length; ++i)
|
||||
Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
|
||||
}
|
||||
for (var i = 0; i < this.length>>1; ++i) {
|
||||
var tmp = this[this.length - i - 1];
|
||||
this[this.length - i - 1] = Bytes.rctab[this[i]];
|
||||
this[i] = Bytes.rctab[tmp];
|
||||
}
|
||||
if (this.length&1)
|
||||
this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
|
||||
}
|
||||
|
||||
if (arguments.length < 2) {
|
||||
print("Usage: k8 sim-pbsim.js <ref.fa.fai> <pbsim1.maf> [[pbsim2.maf] ...]");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
var file, buf = new Bytes(), buf2 = new Bytes();
|
||||
file = new File(arguments[0]);
|
||||
var chr_list = [];
|
||||
while (file.readline(buf) >= 0) {
|
||||
var t = buf.toString().split(/\s+/);
|
||||
chr_list.push(t[0]);
|
||||
}
|
||||
file.close();
|
||||
|
||||
for (var k = 1; k < arguments.length; ++k) {
|
||||
var fn = arguments[k];
|
||||
file = new File(fn);
|
||||
var state = 0, reg;
|
||||
while (file.readline(buf) >= 0) {
|
||||
var line = buf.toString();
|
||||
if (state == 0 && line.charAt(0) == 'a') {
|
||||
state = 1;
|
||||
} else if (state == 1 && line.charAt(0) == 's') {
|
||||
var t = line.split(/\s+/);
|
||||
var st = parseInt(t[2]);
|
||||
reg = [st, st + parseInt(t[3])];
|
||||
state = 2;
|
||||
} else if (state == 2 && line.charAt(0) == 's') {
|
||||
var m, t = line.split(/\s+/);
|
||||
if ((m = /S(\d+)_\d+/.exec(t[1])) == null) throw Error("Failed to parse the read name");
|
||||
var chr_id = parseInt(m[1]) - 1;
|
||||
if (chr_id >= chr_list.length) throw Error("Index outside the chr list");
|
||||
var name = [t[1], chr_list[chr_id], reg[0], reg[1], t[4]].join("!");
|
||||
var seq = t[6].replace(/\-/g, "");
|
||||
if (seq.length != parseInt(t[5])) throw Error("Inconsistent read length");
|
||||
if (seq.indexOf("NN") < 0) {
|
||||
if (t[4] == '-') {
|
||||
buf2.set(seq, 0);
|
||||
buf2.length = seq.length;
|
||||
buf2.revcomp();
|
||||
seq = buf2.toString();
|
||||
}
|
||||
print(">" + name);
|
||||
print(seq);
|
||||
}
|
||||
state = 0;
|
||||
}
|
||||
}
|
||||
file.close();
|
||||
}
|
||||
buf.destroy();
|
||||
buf2.destroy();
|
||||
Loading…
Reference in New Issue