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merged cnt-feat into paftools

This commit is contained in:
Heng Li 2018-02-12 11:29:42 -05:00
parent 50775a1e6f
commit 8c89ba005e
2 changed files with 133 additions and 264 deletions
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258
misc/cnt-feat.js
View File

@ -1,258 +0,0 @@
/*******************************
* Command line option parsing *
*******************************/
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;
}
/***********************
* Interval operations *
***********************/
Interval = {};
Interval.sort = function(a)
{
if (typeof a[0] == 'number')
a.sort(function(x, y) { return x - y });
else a.sort(function(x, y) { return x[0] != y[0]? x[0] - y[0] : x[1] - y[1] });
}
Interval.merge = function(a, sorted)
{
if (typeof sorted == 'undefined') sorted = true;
if (!sorted) Interval.sort(a);
var k = 0;
for (var i = 1; i < a.length; ++i) {
if (a[k][1] >= a[i][0])
a[k][1] = a[k][1] > a[i][1]? a[k][1] : a[i][1];
else a[++k] = a[i].slice(0);
}
a.length = k + 1;
}
Interval.dedup = function(a, sorted)
{
if (typeof sorted == 'undefined') sorted = true;
if (!sorted) Interval.sort(a);
var k = 0;
for (var i = 1; i < a.length; ++i)
if (a[k][0] != a[i][0] || a[k][1] != a[i][1])
a[++k] = a[i].slice(0);
a.length = k + 1;
}
Interval.index_end = function(a, sorted)
{
if (a.length == 0) return;
if (typeof sorted == 'undefined') sorted = true;
if (!sorted) Interval.sort(a);
a[0].push(0);
var k = 0, k_en = a[0][1];
for (var i = 1; i < a.length; ++i) {
if (k_en <= a[i][0]) {
for (++k; k < i; ++k)
if (a[k][1] > a[i][0])
break;
k_en = a[k][1];
}
a[i].push(k);
}
}
Interval.find_intv = function(a, x)
{
var left = -1, right = a.length;
if (typeof a[0] == 'number') {
while (right - left > 1) {
var mid = left + ((right - left) >> 1);
if (a[mid] > x) right = mid;
else if (a[mid] < x) left = mid;
else return mid;
}
} else {
while (right - left > 1) {
var mid = left + ((right - left) >> 1);
if (a[mid][0] > x) right = mid;
else if (a[mid][0] < x) left = mid;
else return mid;
}
}
return left;
}
Interval.find_ovlp = function(a, st, en)
{
if (a.length == 0 || st >= en) return [];
var l = Interval.find_intv(a, st);
var k = l < 0? 0 : a[l][a[l].length - 1];
var b = [];
for (var i = k; i < a.length; ++i) {
if (a[i][0] >= en) break;
else if (st < a[i][1])
b.push(a[i]);
}
return b;
}
/*****************
* Main function *
*****************/
function read_bed(fn, to_merge, to_dedup)
{
var file = new File(fn);
var buf = new Bytes();
var h = {};
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
if (h[t[0]] == null)
h[t[0]] = [];
var bst = parseInt(t[1]);
var ben = parseInt(t[2]);
if (t.length >= 12 && /^\d+$/.test(t[9])) {
t[9] = parseInt(t[9]);
var sz = t[10].split(",");
var st = t[11].split(",");
for (var i = 0; i < t[9]; ++i) {
st[i] = parseInt(st[i]);
sz[i] = parseInt(sz[i]);
h[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
}
} else {
h[t[0]].push([bst, ben, 0, 0, 0]);
}
}
buf.destroy();
file.close();
for (var chr in h) {
if (to_merge) Interval.merge(h[chr], false);
else if (to_dedup) Interval.dedup(h[chr], false);
else Interval.sort(h[chr]);
Interval.index_end(h[chr]);
}
return h;
}
function main(args)
{
var c, print_len = false, to_merge = true, to_dedup = false, fn_excl = null;
while ((c = getopt(args, "pde:")) != null) {
if (c == 'p') print_len = true;
else if (c == 'd') to_dedup = true, to_merge = false;
else if (c == 'e') fn_excl = getopt.arg;
}
if (args.length - getopt.ind < 2) {
print("Usage: k8 cnt-feat.js [options] <target.bed> <feature.bed>");
print("Options:");
print(" -e FILE exclude features overlapping regions in BED FILE []");
print(" -p print number of covered bases for each feature");
exit(1);
}
var excl = fn_excl != null? read_bed(fn_excl, true, false) : null;
var target = read_bed(args[getopt.ind], to_merge, to_dedup);
var file, buf = new Bytes();
var tot_len = 0, hit_len = 0;
file = args[getopt.ind+1] != '-'? new File(args[getopt.ind+1]) : new File();
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
var a = [];
var bst = parseInt(t[1]);
var ben = parseInt(t[2]);
if (t.length >= 12 && /^\d+$/.test(t[9])) { // BED12
t[9] = parseInt(t[9]);
var sz = t[10].split(",");
var st = t[11].split(",");
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], false]);
}
} else a.push([bst, ben, false]); // 3-column BED
var feat_len = 0;
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];
var min_en = o[j][1] < a[i][1]? o[j][1] : a[i][1];
b.push([max_st, min_en]);
o[j][2] += min_en - max_st;
++o[j][3];
if (max_st == o[j][0] && min_en == o[j][1])
++o[j][4];
}
}
// find the length covered
var feat_hit_len = 0;
if (b.length > 0) {
b.sort(function(a,b) {return a[0]-b[0]});
var st = b[0][0], en = b[0][1];
for (var i = 1; i < b.length; ++i) {
if (b[i][0] <= en) en = en > b[i][1]? en : b[i][1];
else feat_hit_len += en - st, st = b[i][0], en = b[i][1];
}
feat_hit_len += en - st;
}
hit_len += feat_hit_len;
if (print_len) print('F', t.slice(0, 4).join("\t"), feat_len, feat_hit_len);
}
file.close();
buf.destroy();
warn("# feature bases: " + tot_len);
warn("# feature bases overlapping targets: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
}
main(arguments);

139
misc/paftools.js
View File

@ -618,6 +618,127 @@ function paf_stat(args)
}
}
function paf_bedcov(args)
{
function read_bed(fn, to_merge, to_dedup)
{
var file = new File(fn);
var buf = new Bytes();
var h = {};
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
if (h[t[0]] == null)
h[t[0]] = [];
var bst = parseInt(t[1]);
var ben = parseInt(t[2]);
if (t.length >= 12 && /^\d+$/.test(t[9])) {
t[9] = parseInt(t[9]);
var sz = t[10].split(",");
var st = t[11].split(",");
for (var i = 0; i < t[9]; ++i) {
st[i] = parseInt(st[i]);
sz[i] = parseInt(sz[i]);
h[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
}
} else {
h[t[0]].push([bst, ben, 0, 0, 0]);
}
}
buf.destroy();
file.close();
for (var chr in h) {
if (to_merge) Interval.merge(h[chr], false);
else if (to_dedup) Interval.dedup(h[chr], false);
else Interval.sort(h[chr]);
Interval.index_end(h[chr]);
}
return h;
}
var c, print_len = false, to_merge = true, to_dedup = false, fn_excl = null;
while ((c = getopt(args, "pde:")) != null) {
if (c == 'p') print_len = true;
else if (c == 'd') to_dedup = true, to_merge = false;
else if (c == 'e') fn_excl = getopt.arg;
}
if (args.length - getopt.ind < 2) {
print("Usage: paftools.js bedcov [options] <regions.bed> <target.bed>");
print("Options:");
print(" -e FILE exclude target regions (2nd file) overlapping BED FILE []");
print(" -p print number of covered bases for each target");
exit(1);
}
var excl = fn_excl != null? read_bed(fn_excl, true, false) : null;
var target = read_bed(args[getopt.ind], to_merge, to_dedup);
var file, buf = new Bytes();
var tot_len = 0, hit_len = 0;
file = args[getopt.ind+1] != '-'? new File(args[getopt.ind+1]) : new File();
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
var a = [];
var bst = parseInt(t[1]);
var ben = parseInt(t[2]);
if (t.length >= 12 && /^\d+$/.test(t[9])) { // BED12
t[9] = parseInt(t[9]);
var sz = t[10].split(",");
var st = t[11].split(",");
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], false]);
}
} else a.push([bst, ben, false]); // 3-column BED
var feat_len = 0;
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];
var min_en = o[j][1] < a[i][1]? o[j][1] : a[i][1];
b.push([max_st, min_en]);
o[j][2] += min_en - max_st;
++o[j][3];
if (max_st == o[j][0] && min_en == o[j][1])
++o[j][4];
}
}
// find the length covered
var feat_hit_len = 0;
if (b.length > 0) {
b.sort(function(a,b) {return a[0]-b[0]});
var st = b[0][0], en = b[0][1];
for (var i = 1; i < b.length; ++i) {
if (b[i][0] <= en) en = en > b[i][1]? en : b[i][1];
else feat_hit_len += en - st, st = b[i][0], en = b[i][1];
}
feat_hit_len += en - st;
}
hit_len += feat_hit_len;
if (print_len) print('F', t.slice(0, 4).join("\t"), feat_len, feat_hit_len);
}
file.close();
buf.destroy();
warn("# feature bases: " + tot_len);
warn("# feature bases overlapping targets: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
}
/**************************
*** Conversion related ***
**************************/
@ -1047,7 +1168,7 @@ function paf_splice2bed(args)
{
var colors = ["0,128,255", "255,0,0", "0,192,0"];
function print_lines(a, fmt)
function print_lines(a, fmt, keep_multi)
{
if (a.length == 0) return;
if (fmt == "bed") {
@ -1061,6 +1182,7 @@ function paf_splice2bed(args)
warn("Warning: " + a[0][3] + " doesn't have a primary alignment");
}
for (var i = 0; i < a.length; ++i) {
if (!keep_multi && a[i][8] == 2) continue;
a[i][8] = colors[a[i][8]];
print(a[i].join("\t"));
}
@ -1069,13 +1191,16 @@ function paf_splice2bed(args)
}
var re = /(\d+)([MIDNSH])/g;
var c, fmt = "bed", fn_name_conv = null;
while ((c = getopt(args, "f:n:")) != null) {
var c, fmt = "bed", fn_name_conv = null, keep_multi = false;
while ((c = getopt(args, "f:n:m")) != null) {
if (c == 'f') fmt = getopt.arg;
else if (c == 'n') fn_name_conv = getopt.arg;
else if (c == 'm') keep_multi = true;
}
if (getopt.ind == args.length) {
warn("Usage: paftools.js splice2bed <in.paf>|<in.sam>");
print("Usage: paftools.js splice2bed [options] <in.paf>|<in.sam>");
print("Options:");
print(" -m keep multiple mappings (SAM flag 0x100)");
exit(1);
}
@ -1107,7 +1232,7 @@ function paf_splice2bed(args)
if (flag&1) t[0] += '/' + (flag>>6&3);
}
if (a.length && a[0][3] != t[0]) {
print_lines(a, fmt);
print_lines(a, fmt, keep_multi);
a = [];
}
if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) { // PAF
@ -1148,7 +1273,7 @@ function paf_splice2bed(args)
a1.push(is_pri? 0 : 2, bs.length, bl.join(",")+",", bs.join(",")+",");
a.push(a1);
}
print_lines(a, fmt);
print_lines(a, fmt, keep_multi);
buf.destroy();
file.close();
if (conv != null) conv.destroy();
@ -1707,6 +1832,7 @@ function main(args)
print(" stat collect basic mapping information in PAF/SAM");
print(" liftover simplistic liftOver");
print(" call call variants from asm-to-ref alignment with the cs tag");
print(" bedcov compute the number of bases covered");
print("");
print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
print(" mason2fq convert mason2-simulated SAM to FASTQ");
@ -1726,6 +1852,7 @@ function main(args)
else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
else if (cmd == 'call') paf_call(args);
else if (cmd == 'mapeval') paf_mapeval(args);
else if (cmd == 'bedcov') paf_bedcov(args);
else if (cmd == 'mason2fq') paf_mason2fq(args);
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
else if (cmd == 'junceval') paf_junceval(args);