From 024195db629662c892303e9bac5daf853dd1e7b6 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 5 May 2014 16:51:14 -0400 Subject: [PATCH] code backup --- bwa-helper.js | 239 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 238 insertions(+), 1 deletion(-) diff --git a/bwa-helper.js b/bwa-helper.js index e904fc2..e691967 100644 --- a/bwa-helper.js +++ b/bwa-helper.js @@ -2,7 +2,7 @@ * The K8 Javascript interpreter is required to run this script. * * * * Source code: https://github.com/attractivechaos/k8 * - * Binary: https://sourceforge.net/projects/lh3/files/ * + * Binary: http://sourceforge.net/projects/lh3/files/k8/ * *****************************************************************/ /****************** @@ -338,6 +338,242 @@ function bwa_gff2sam(args) file.close(); } + +/****************************** + *** Generate ALT alignment *** + ******************************/ + +function intv_ovlp(intv, bits) // interval index +{ + if (typeof bits == "undefined") bits = 13; + intv.sort(function(a,b) {return a[0]-b[0];}); + // create the index + var idx = [], max = 0; + for (var i = 0; i < intv.length; ++i) { + var b = intv[i][0]>>bits; + var e = (intv[i][1]-1)>>bits; + if (b != e) { + for (var j = b; j <= e; ++j) + if (idx[j] == null) idx[j] = i; + } else if (idx[b] == null) idx[b] = i; + max = max > e? max : e; + } + // closure + return function(_b, _e, is_contained) { + var x = _b >> bits; + if (x > max) return []; + var off = idx[x]; + if (off == null) { + var i; + for (i = ((_e - 1) >> bits) - 1; i >= 0; --i) + if (idx[i] != null) break; + off = i < 0? 0 : idx[i]; + } + var ovlp = []; + if (!is_contained) { + for (var i = off; i < intv.length && intv[i][0] < _e; ++i) + if (intv[i][1] > _b) ovlp.push(intv[i]); + } else { + for (var i = off; i < intv.length && intv[i][1] <= _e; ++i) + if (intv[i][0] >= _b) ovlp.push(intv[i]); + } + return ovlp; + } +} + +function bwa_genalt(args) +{ + function cigar2pos(cigar, pos) + { + var x = 0, y = 0; + for (var i = 0; i < cigar.length; ++i) { + var op = cigar[i][0], len = cigar[i][1]; + if (op == 'M') { + if (y <= pos && pos < y + len) + return x + (pos - y); + x += len, y += len; + } else if (op == 'D') { + x += len; + } else if (op == 'I') { + if (y <= pos && pos < y + len) + return x; + y += len; + } else if (op == 'S' || op == 'H') { + if (y <= pos && pos < y + len) + return -1; + y += len; + } + } + return -1; + } + + var opt = { a:1, b:4, o:6, e:1 }; + + if (args.length == 0) { + print("Usage: k8 bwa-helper.js genalt [aln.sam]"); + exit(1); + } + + var re_cigar = /(\d+)([MIDSHN])/g; + var file, buf = new Bytes(); + + // read the ALT-to-REF alignment and generate the index + var intv = {}; + file = new File(args[0]); + while (file.readline(buf) >= 0) { + var line = buf.toString(); + var t = line.split("\t"); + if (line.charAt(0) == '@') continue; + var flag = parseInt(t[1]); + var m, cigar = [], l_qaln = 0, l_qclip = 0; + while ((m = re_cigar.exec(t[5])) != null) { + var l = parseInt(m[1]); + cigar.push([m[2] != 'H'? m[2] : 'S', l]); // convert hard clip to soft clip + if (m[2] == 'M' || m[2] == 'I') l_qaln += l; + else if (m[2] == 'S' || m[2] == 'H') l_qclip += l; + } + var j = flag&16? cigar.length-1 : 0; + var start = cigar[j][0] == 'S'? cigar[j][1] : 0; + if (intv[t[0]] == null) intv[t[0]] = []; + intv[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]); + //print(start, start + l_qaln, t[2], flag&16? true : false, parseInt(t[3]), cigar); + } + file.close(); + + var idx = {}; + for (var ctg in intv) + idx[ctg] = intv_ovlp(intv[ctg]); + + // process SAM + file = args.length >= 2? new File(args[1]) : new File(); + while (file.readline(buf) >= 0) { + var m, line = buf.toString(); + if (line.charAt(0) == '@' || (m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file + //print(line); + continue; + } + + // parse hits + var XA_strs = m[1].split(";"); + var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? 0 : parseInt(m[1]); + var t = line.split("\t"); + // a hit element: [0:chr, 1:isRev, 2:start, 3:end, 4:cigar, 5:NM, 6:score, 7+:"lifted info"] + var hits = [[t[2], (parseInt(t[1]) & 16)? true : false, parseInt(t[3]) - 1, 0, t[5], NM]]; // the major hit + for (var i = 0; i < XA_strs.length; ++i) { // hits in the XA tag + if (XA_strs[i] == '') continue; // if the last char is ';', we will have an empty string + var s = XA_strs[i].split(","); + hits.push([s[0], s[1].charAt(0) == '-'? true : false, parseInt(s[1].substr(1)) - 1, 0, s[2], parseInt(s[3])]); + } + + // lift mapping positions to the coordinates on the primary assembly + var n_lifted = 0; + for (var i = 0; i < hits.length; ++i) { + var h = hits[i]; + + // parse the cigar + var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip; + l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0; + while ((m = re_cigar.exec(h[4])) != null) { + var l = parseInt(m[1]); + if (m[2] == 'M') l_match += l; + else if (m[2] == 'D') ++n_del, l_del += l; + else if (m[2] == 'I') ++n_ins, l_ins += l; + else if (m[2] == 'N') l_skip += l; + else if (m[2] == 'H' || m[2] == 'S') l_clip += l; + } + h[3] = h[2] + l_match + l_del + l_skip; + h[5] = h[5] > l_del + l_ins? h[5] : l_del + l_ins; + var score = opt.a * l_match - (opt.a + opt.b) * (h[5] - l_del - l_ins) - opt.o * (n_del + n_ins) - opt.e * (l_del + l_ins); + h.push(score); + + if (idx[h[0]] == null) continue; + var a = idx[h[0]](h[2], h[3]); + if (a == null || a.length == 0) continue; + + // find the approximate position on the primary assembly + var regs = []; + for (var j = 0; j < a.length; ++j) { + var s, e; + if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly + s = cigar2pos(a[j][6], h[2]); + e = cigar2pos(a[j][6], h[3] - 1) + 1; + } else { + s = cigar2pos(a[j][6], a[j][2] - h[3]); + e = cigar2pos(a[j][6], a[j][2] - h[2] - 1) + 1; + } + if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment + s += a[j][5]; e += a[j][5]; + //print("*", a[j][4], h[0], a[j][3], s, e); + regs.push([a[j][3], (h[1]!=a[j][4]), s, e]); + } + if (regs.length == 0) continue; + hits[i].push(regs[0][0], regs[0][1], regs[0][2], regs[0][3]); // TODO: regs.length may be larger than one, though this occurs rarely + ++n_lifted; + } + if (n_lifted == 0) { + //print(line); + continue; + } + + // group hits + var phits = []; + for (var i = 0; i < hits.length; ++i) { + var h = hits[i]; + if (h.length > 7) phits.push([h[7], h[9], h[10], -1]); // lifted + else phits.push([h[0], h[2], h[3], -1]); + } + phits.sort(function(a,b) { + if (a[0] != b[0]) return a[0] < b[0]? -1 : 1; + if (a[1] != b[1]) return a[1] - b[1]; + }); + var last_chr = null, end = 0, groupid = -1; + for (var i = 0; i < phits.length; ++i) { + if (last_chr != phits[i][0]) { // change of chr + phits[i][3] = ++groupid; + last_chr = phits[i][0], end = phits[i][2]; + } else if (phits[i][1] >= end) { // no overlap + phits[i][3] = ++groupid; + end = phits[i][2]; + } else { + phits[i][3] = groupid; + end = end > phits[i][2]? end : phits[i][2]; + } + } + var n_group0 = 0; // #hits overlapping the reported hit + for (var i = 0; i < phits.length; ++i) + if (phits[i][3] == phits[0][3]) + ++n_group0; + if (n_group0 == 1) { // then keep the reported alignment and mapQ + //print(line); + continue; + } + + // re-estimate mapQ + var group_max = []; + for (var i = 0; i < phits.length; ++i) + if (group_max[phits[i][3]] == null || group_max[phits[i][3]][0] < hits[i][6]) + group_max[phits[i][3]] = [hits[i][6], phits[i][3]]; + if (group_max.length > 1) + group_max.sort(function(x,y) {return y[0]-x[0]}); + var mapQ; + if (group_max[0][1] == phits[0][3]) { // the best hit is the hit reported in SAM + mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]); + } else mapQ = 0; + mapQ = mapQ < 60? mapQ : 60; + var ori_mapQ = parseInt(t[4]); + mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ; + + t[4] = mapQ; + print(t.join("\t")); + print("*", mapQ); + for (var i = 0; i < hits.length; ++i) + print(hits[i]); + } + file.close(); + + buf.destroy(); +} + /********************* *** Main function *** *********************/ @@ -362,6 +598,7 @@ function main(args) else if (cmd == 'markovlp') bwa_markOvlp(args); else if (cmd == 'pas2reg') bwa_pas2reg(args); else if (cmd == 'reg2cut') bwa_reg2cut(args); + else if (cmd == 'genalt') bwa_genalt(args); else if (cmd == 'shortname') bwa_shortname(args); else warn("Unrecognized command"); }