82 lines
2.2 KiB
JavaScript
82 lines
2.2 KiB
JavaScript
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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if (arguments.length < 2) {
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print("Usage: k8 pbsim2paf.js <chr.list> <pbsim1.maf> [[pbsim2.maf] ...]");
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exit(1);
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}
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var file, buf = new Bytes(), buf2 = new Bytes();
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file = new File(arguments[0]);
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var chr_list = [];
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while (file.readline(buf) >= 0) {
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var t = buf.toString().split(/\s+/);
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chr_list.push(t[0]);
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}
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file.close();
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for (var k = 1; k < arguments.length; ++k) {
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var fn = arguments[k];
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file = new File(fn);
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var state = 0, reg;
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while (file.readline(buf) >= 0) {
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var line = buf.toString();
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if (state == 0 && line.charAt(0) == 'a') {
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state = 1;
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} else if (state == 1 && line.charAt(0) == 's') {
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var t = line.split(/\s+/);
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var st = parseInt(t[2]);
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reg = [st, st + parseInt(t[3])];
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state = 2;
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} else if (state == 2 && line.charAt(0) == 's') {
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var m, t = line.split(/\s+/);
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if ((m = /S(\d+)_\d+/.exec(t[1])) == null) throw Error("Failed to parse the read name");
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var chr_id = parseInt(m[1]) - 1;
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if (chr_id >= chr_list.length) throw Error("Index outside the chr list");
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var name = [t[1], chr_list[chr_id], reg[0], reg[1], t[4]].join("!");
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var seq = t[6].replace(/\-/g, "");
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if (seq.length != parseInt(t[5])) throw Error("Inconsistent read length");
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if (seq.indexOf("NN") < 0) {
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if (t[4] == '-') {
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buf2.set(seq, 0);
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buf2.length = seq.length;
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buf2.revcomp();
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seq = buf2.toString();
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}
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print(">" + name);
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print(seq);
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}
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state = 0;
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}
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}
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file.close();
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}
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buf.destroy();
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buf2.destroy();
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