added utg error correction
This commit is contained in:
Heng Li
parent
cd2b19035b
commit
28a37a017a
|
|
@ -0,0 +1,306 @@
|
|||
#!/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;
|
||||
}
|
||||
|
||||
function read_fastx(file, buf)
|
||||
{
|
||||
if (file.readline(buf) < 0) return null;
|
||||
var m, line = buf.toString();
|
||||
if ((m = /^([>@])(\S+)/.exec(line)) == null)
|
||||
throw Error("wrong fastx format");
|
||||
var is_fq = (m[1] == '@');
|
||||
var name = m[2];
|
||||
if (file.readline(buf) < 0)
|
||||
throw Error("missing sequence line");
|
||||
var seq = buf.toString();
|
||||
if (is_fq) { // skip quality
|
||||
file.readline(buf);
|
||||
file.readline(buf);
|
||||
}
|
||||
return [name, seq];
|
||||
}
|
||||
|
||||
function filter_paf(a, opt)
|
||||
{
|
||||
if (a.length == 0) return;
|
||||
var k = 0;
|
||||
for (var i = 0; i < a.length; ++i) {
|
||||
var ai = a[i];
|
||||
if (ai[10] < opt.min_blen) continue;
|
||||
if (ai[9] < ai[10] * opt.min_iden) continue;
|
||||
var clip = [0, 0];
|
||||
if (ai[4] == '+') {
|
||||
clip[0] = ai[2] < ai[7]? ai[2] : ai[7];
|
||||
clip[1] = ai[1] - ai[3] < ai[6] - ai[8]? ai[1] - ai[3] : ai[6] - ai[8];
|
||||
} else {
|
||||
clip[0] = ai[2] < ai[6] - ai[8]? ai[2] : ai[6] - ai[8];
|
||||
clip[1] = ai[1] - ai[3] < ai[7]? ai[1] - ai[3] : ai[7];
|
||||
}
|
||||
if (clip[0] > opt.max_clip_len || clip[1] > opt.max_clip_len) continue;
|
||||
a[k++] = ai;
|
||||
}
|
||||
a.length = k;
|
||||
}
|
||||
|
||||
function parse_events(t, ev, id, buf)
|
||||
{
|
||||
var re = /(:(\d+))|(([\+\-\*])([a-z]+))/g;
|
||||
var m, cs = null;
|
||||
for (var j = 12; j < t.length; ++j) {
|
||||
if ((m = /^cs:Z:(\S+)/.exec(t[j])) != null) {
|
||||
cs = m[1].toLowerCase();
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (cs == null) {
|
||||
warn("Warning: no cs tag for read '" + t[0] + "'");
|
||||
return;
|
||||
}
|
||||
var st = t[2], en = t[3];
|
||||
var x = st;
|
||||
while ((m = re.exec(cs)) != null) {
|
||||
var l;
|
||||
if (m[2] != null) {
|
||||
l = parseInt(m[2]);
|
||||
ev.push([x, x + l, 0, id]);
|
||||
} else {
|
||||
if (m[4] == '*') {
|
||||
l = 1;
|
||||
ev.push([x, x + 1, 1, id, m[5][0]]);
|
||||
} else if (m[4] == '+') {
|
||||
l = m[5].length;
|
||||
ev.push([x, x + l, 2, id]);
|
||||
} else if (m[4] == '-') {
|
||||
l = 0;
|
||||
ev.push([x, x, -1, id, m[5]]);
|
||||
}
|
||||
}
|
||||
x += l;
|
||||
}
|
||||
if (x != en)
|
||||
throw Error("inconsistent cs for read '" + t[0] + "'");
|
||||
}
|
||||
|
||||
function find_het_sub(ev, a, opt)
|
||||
{
|
||||
var n = a.length, last0_i = -1, h = [], d = [];
|
||||
for (var i = 0; i < n; ++i) h[i] = [], d[i] = [];
|
||||
for (var i = 0; i < ev.length; ++i) {
|
||||
if (ev[i][2] == 0) {
|
||||
if (last0_i < 0 || ev[i][0] != ev[last0_i][0]) last0_i = i;
|
||||
else if (ev[i][1] > ev[last0_i][1])
|
||||
last0_i = i;
|
||||
} else if (ev[i][2] == 1 && last0_i >= 0 && ev[i][0] < ev[last0_i][1]) {
|
||||
if (ev[last0_i][1] - ev[last0_i][0] >= opt.min_mlen) {
|
||||
//print(ev[last0_i].join("\t"), "|", ev[i].join("\t"));
|
||||
var e0 = ev[last0_i], hl = h[e0[3]];
|
||||
if (hl.length == 0 || hl[hl.length-1][0] != e0[0])
|
||||
hl.push([e0[0], e0[1]]);
|
||||
d[ev[i][3]].push([ev[i][0], e0[1] - e0[0]]);
|
||||
}
|
||||
}
|
||||
}
|
||||
var b = [];
|
||||
for (var i = 0; i < n; ++i) {
|
||||
var sh = 0, dh = 0;
|
||||
for (var j = 0; j < h[i].length; ++j)
|
||||
sh += h[i][j][1] - h[i][j][0];
|
||||
for (var j = 0; j < d[i].length; ++j)
|
||||
dh += d[i][j][1];
|
||||
b[i] = [a[i][2], a[i][3], i, h[i].length, sh, d[i].length, dh, a[i][9] / a[i][10], a[i][9]];
|
||||
}
|
||||
return b;
|
||||
}
|
||||
|
||||
function flt_utg(b, opt)
|
||||
{
|
||||
var k = 0;
|
||||
for (var i = 0; i < b.length; ++i) {
|
||||
var bi = b[i];
|
||||
if (bi[4] == 0 && bi[6] == 0) b[k++] = bi;
|
||||
else if (bi[6] < (bi[4] + bi[6]) * opt.max_ratio0) b[k++] = bi;
|
||||
}
|
||||
b.length = k;
|
||||
if (b.length == 0) return;
|
||||
// find the longest contiguous segment
|
||||
b.sort(function(x,y) { return x[0]-y[0] });
|
||||
var st = b[0][0], en = b[0][1], max_st = 0, max_en = 0, max_max_en = en;
|
||||
for (var i = 1; i < b.length; ++i) {
|
||||
if (b[i][0] > en) {
|
||||
if (en - st > max_en - max_st)
|
||||
max_st = st, max_en = en;
|
||||
st = b[i][0], en = b[i][1];
|
||||
} else {
|
||||
en = en > b[i][1]? en : b[i][1];
|
||||
}
|
||||
max_max_en = max_max_en > b[i][1]? max_max_en : b[i][1];
|
||||
}
|
||||
if (en - st > max_en - max_st)
|
||||
max_st = st, max_en = en;
|
||||
if (max_max_en != en || st != b[0][0]) {
|
||||
var k = 0;
|
||||
for (var i = 0; i < b.length; ++i)
|
||||
if (b[i][0] < max_en && b[i][1] > max_st)
|
||||
b[k++] = b[i];
|
||||
b.length = k;
|
||||
}
|
||||
}
|
||||
|
||||
function ec_core(b, n_a, ev, buf, ecb)
|
||||
{
|
||||
var intv = [];
|
||||
for (var i = 0; i < n_a; ++i)
|
||||
intv[i] = null;
|
||||
intv[b[0][2]] = [b[0][0], b[0][1]];
|
||||
var en = b[0][1];
|
||||
for (var i = 1; i < b.length; ++i) {
|
||||
if (b[i][1] <= en) continue;
|
||||
intv[b[i][2]] = [en, b[i][1]];
|
||||
en = b[i][1];
|
||||
}
|
||||
var k = 0;
|
||||
ecb.capacity = buf.capacity;
|
||||
ecb.length = 0;
|
||||
for (var i = 0; i < ev.length; ++i) {
|
||||
var e = ev[i], I = intv[e[3]];
|
||||
if (I == null) continue;
|
||||
if (e[0] >= I[0] && e[0] < I[1]) { // this is to reduce duplicated events around junctions
|
||||
//print("X", e.join("\t"));
|
||||
if (e[2] == 0) {
|
||||
ecb.length += e[1] - e[0];
|
||||
for (var j = e[0]; j < e[1]; ++j)
|
||||
ecb[k++] = buf[j];
|
||||
} else if (e[2] == 1) {
|
||||
++ecb.length;
|
||||
ecb[k++] = e[4].charCodeAt(0);
|
||||
} else if (e[2] < 0) {
|
||||
ecb.length += e[4].length;
|
||||
for (var j = 0; j < e[4].length; ++j)
|
||||
ecb[k++] = e[4].charCodeAt(j);
|
||||
} // else, skip e[2] == 2
|
||||
}
|
||||
}
|
||||
if (ecb.length != k) throw Error("BUG!");
|
||||
}
|
||||
|
||||
function process_paf(a, opt, fp_seq, buf, ecb)
|
||||
{
|
||||
if (a.length == 0) return;
|
||||
var len = a[0][1];
|
||||
if (len < opt.min_rlen) return;
|
||||
var ret;
|
||||
while ((ret = read_fastx(fp_seq, buf, name, seq)) != null)
|
||||
if (ret[0] == a[0][0])
|
||||
break;
|
||||
if (ret == null)
|
||||
throw Error("failed to find sequence for read '" + a[0][0] + "'");
|
||||
var name = ret[0], seq = ret[1], len = a[0][1];
|
||||
if (seq.length != len)
|
||||
throw Error("inconsistent length for read '" + name + "'");
|
||||
filter_paf(a, opt);
|
||||
if (a.length == 0) return;
|
||||
var ev = [];
|
||||
for (var i = 0; i < a.length; ++i)
|
||||
parse_events(a[i], ev, i, buf);
|
||||
ev.sort(function(x,y) { return x[0]!=y[0]? x[0]-y[0] : x[2]-y[2] });
|
||||
if (opt.dbg)
|
||||
print(">"+name, a[0][1], a.length);
|
||||
var b = find_het_sub(ev, a, opt);
|
||||
flt_utg(b, opt);
|
||||
if (b.length == 0) return;
|
||||
buf.set(seq, 0);
|
||||
ec_core(b, a.length, ev, buf, ecb);
|
||||
if (opt.dbg) {
|
||||
for (var i = 0; i < b.length; ++i)
|
||||
print(b[i].join("\t"), a[b[i][2]][5]);
|
||||
} else {
|
||||
print(">" + name);
|
||||
print(ecb);
|
||||
}
|
||||
}
|
||||
|
||||
function main(args)
|
||||
{
|
||||
var c, opt = { min_rlen:20000, min_blen:10000, min_iden:0.8, min_mlen:5, max_clip_len:500, max_ratio0:0.25, dbg:false };
|
||||
while ((c = getopt(args, "l:b:d:m:c:r:D")) != null) {
|
||||
if (c == 'l') opt.min_rlen = parseInt(getopt.arg);
|
||||
else if (c == 'b') opt.min_blen = parseInt(getopt.arg);
|
||||
else if (c == 'd') opt.min_iden = parseFloat(getopt.arg);
|
||||
else if (c == 'm') opt.min_slen = parseInt(getopt.arg);
|
||||
else if (c == 'c') opt.max_clip_len = parseInt(getopt.arg);
|
||||
else if (c == 'r') opt.max_ratio0 = parseFloat(getopt.arg);
|
||||
else if (c == 'D') opt.dbg = true;
|
||||
}
|
||||
if (args.length - getopt.ind < 2) {
|
||||
print("Usage: utec.js [options] <map-with-cs.paf> <seq.fa>");
|
||||
print("Options:");
|
||||
print(" -l INT min read length [" + opt.min_rlen + "]");
|
||||
print(" -b INT min alignment length [" + opt.min_blen + "]");
|
||||
print(" -d FLOAT min identity [" + opt.min_iden + "]");
|
||||
print(" -s INT min match length [" + opt.min_mlen + "]");
|
||||
print(" -c INT max clip length [" + opt.max_clip_len + "]");
|
||||
print(" -r FLOAT initial ratio for haplotype filtering [" + opt.max_ratio0 + "]");
|
||||
return 0;
|
||||
}
|
||||
var buf = new Bytes(), ecb = new Bytes();
|
||||
var fp_paf = new File(args[getopt.ind]);
|
||||
var fp_seq = new File(args[getopt.ind+1]);
|
||||
var a = [];
|
||||
while (fp_paf.readline(buf) >= 0) {
|
||||
var t = buf.toString().split("\t");
|
||||
if (a.length > 0 && a[0][0] != t[0]) {
|
||||
process_paf(a, opt, fp_seq, buf, ecb);
|
||||
a.length = 0;
|
||||
}
|
||||
for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]);
|
||||
if (t[1] < opt.min_rlen) continue;
|
||||
for (var i = 6; i <= 10; ++i) t[i] = parseInt(t[i]);
|
||||
if (t[10] < opt.min_blen) continue;
|
||||
a.push(t);
|
||||
}
|
||||
if (a.length >= 0)
|
||||
process_paf(a, opt, fp_seq, buf, ecb);
|
||||
fp_seq.close();
|
||||
fp_paf.close();
|
||||
ecb.destroy();
|
||||
buf.destroy();
|
||||
}
|
||||
|
||||
var ret = main(arguments)
|
||||
exit(ret)
|
||||
Loading…
Reference in New Issue