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allow to exclude regions

This commit is contained in:
Heng Li 2018-01-07 22:35:56 -05:00
parent f5cfd439ee
commit 1842d7f5b5
1 changed files with 49 additions and 33 deletions
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82
misc/cnt-feat.js
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@ -134,27 +134,15 @@ Interval.find_ovlp = function(a, st, en)
* Main function *
*****************/
function main(args)
function read_bed(fn, to_merge, to_dedup)
{
var c, print_len = false, to_merge = true, to_dedup = false;
while ((c = getopt(args, "pd")) != null) {
if (c == 'p') print_len = true;
else if (c == 'd') to_dedup = true, to_merge = false;
}
if (args.length - getopt.ind < 2) {
print("Usage: k8 cnt-feat.js [options] <target.bed> <feature.bed>");
exit(1);
}
var file, buf = new Bytes();
var target = {};
file = new File(args[getopt.ind]);
var file = new File(fn);
var buf = new Bytes();
var h = {};
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
if (target[t[0]] == null)
target[t[0]] = [];
if (h[t[0]] == null)
h[t[0]] = [];
var bst = parseInt(t[1]);
var ben = parseInt(t[2]);
if (t.length >= 12 && /^\d+$/.test(t[9])) {
@ -164,26 +152,46 @@ function main(args)
for (var i = 0; i < t[9]; ++i) {
st[i] = parseInt(st[i]);
sz[i] = parseInt(sz[i]);
target[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
h[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
}
} else {
target[t[0]].push([bst, ben, 0, 0, 0]);
h[t[0]].push([bst, ben, 0, 0, 0]);
}
}
buf.destroy();
file.close();
var n_target_intv = 0;
for (var chr in target) {
if (to_merge) Interval.merge(target[chr], false);
else if (to_dedup) Interval.dedup(target[chr], false);
else Interval.sort(target[chr]);
n_target_intv += target[chr].length;
Interval.index_end(target[chr]);
for (var chr in h) {
if (to_merge) Interval.merge(h[chr], false);
else if (to_dedup) Interval.dedup(h[chr], false);
else Interval.sort(h[chr]);
Interval.index_end(h[chr]);
}
warn("# target intervals: " + n_target_intv);
return h;
}
function main(args)
{
var c, print_len = false, to_merge = true, to_dedup = false, fn_excl = null;
while ((c = getopt(args, "pde:")) != null) {
if (c == 'p') print_len = true;
else if (c == 'd') to_dedup = true, to_merge = false;
else if (c == 'e') fn_excl = getopt.arg;
}
if (args.length - getopt.ind < 2) {
print("Usage: k8 cnt-feat.js [options] <target.bed> <feature.bed>");
print("Options:");
print(" -e FILE exclude features overlapping regions in BED FILE []");
print(" -p print number of covered bases for each feature");
exit(1);
}
var excl = fn_excl != null? read_bed(fn_excl, true, false) : null;
var target = read_bed(args[getopt.ind], to_merge, to_dedup);
var file, buf = new Bytes();
var tot_len = 0, hit_len = 0;
file = new File(args[getopt.ind+1]);
file = args[getopt.ind+1] != '-'? new File(args[getopt.ind+1]) : new File();
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
var a = [];
@ -196,16 +204,24 @@ function main(args)
for (var i = 0; i < t[9]; ++i) {
st[i] = parseInt(st[i]);
sz[i] = parseInt(sz[i]);
a.push([bst + st[i], bst + st[i] + sz[i]]);
a.push([bst + st[i], bst + st[i] + sz[i], false]);
}
} else a.push([bst, ben]); // 3-column BED
} else a.push([bst, ben, false]); // 3-column BED
var feat_len = 0;
for (var i = 0; i < a.length; ++i)
for (var i = 0; i < a.length; ++i) {
if (excl != null && excl[t[0]] != null) {
var oe = Interval.find_ovlp(excl[t[0]], a[i][0], a[i][1]);
if (oe.length > 0)
continue;
}
a[i][2] = true;
feat_len += a[i][1] - a[i][0];
}
tot_len += feat_len;
if (target[t[0]] == null) continue;
var b = [];
for (var i = 0; i < a.length; ++i) {
if (!a[i][2]) continue;
var o = Interval.find_ovlp(target[t[0]], a[i][0], a[i][1]);
for (var j = 0; j < o.length; ++j) {
var max_st = o[j][0] > a[i][0]? o[j][0] : a[i][0];