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hidden options to control bp calculation

This commit is contained in:
Heng Li 2018-11-04 16:36:04 -05:00
parent 42baf287a4
commit e315b9fada
1 changed files with 41 additions and 13 deletions
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54
misc/paftools.js
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@ -564,10 +564,12 @@ function paf_call(args)
function paf_asmstat(args)
{
var c, min_seg_len = 10000, max_diff = 0.01;
while ((c = getopt(args, "l:d:")) != null) {
var c, min_seg_len = 10000, max_diff = 0.01, bp_flank_len = 0, bp_gap_len = 0;
while ((c = getopt(args, "l:d:b:g:")) != null) {
if (c == 'l') min_seg_len = parseInt(getopt.arg);
else if (c == 'd') max_diff = parseFloat(getopt.arg);
else if (c == 'b') bp_flank_len = parseInt(getopt.arg);
else if (c == 'g') bp_gap_len = parseInt(getopt.arg);
}
if (getopt.ind == args.length) {
print("Usage: paftools.js asmstat [options] <ref.fa.fai> <asm1.paf> [...]");
@ -587,7 +589,7 @@ function paf_asmstat(args)
}
file.close();
function process_query(qblocks, qblock_len, bp) {
function process_query(qblocks, qblock_len, bp, qi) {
qblocks.sort(function(a,b) { return a[0]-b[0]; });
var last_k = null, last_blen = null, st = -1, en = -1, qcov = 0;
for (var k = 0; k < qblocks.length; ++k) {
@ -612,6 +614,7 @@ function paf_asmstat(args)
var min = blen < last_blen? blen : last_blen;
var flank = k == 0? min : blen;
bp.push([flank, gap]);
qi.bp.push([flank, gap]);
}
last_k = k, last_blen = blen;
}
@ -664,16 +667,22 @@ function paf_asmstat(args)
for (var i = 0; i < n_asm; ++i) {
var n_breaks = 0, qcov = 0;
var fn = args[getopt.ind + 1 + i];
header.push(fn.replace(/.paf(.gz)?$/, ""));
var label = fn.replace(/.paf(.gz)?$/, "");
header.push(label);
var ref_blocks = [], qblock_len = [], qblocks = [], bp = [];
var query = {};
var query = {}, qinfo = {};
var last_qname = null;
file = new File(fn);
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
var t = line.split("\t");
t[1] = parseInt(t[1]);
if (t.length >= 2) query[t[0]] = t[1];
if (t.length >= 2) {
query[t[0]] = t[1];
if (qinfo[t[0]] == null) qinfo[t[0]] = {};
qinfo[t[0]].len = t[1];
qinfo[t[0]].bp = [];
}
if (t.length < 9) continue;
if (!/\ttp:A:[PI]/.test(line)) continue;
if ((m = /\tcg:Z:(\S+)/.exec(line)) == null) continue;
@ -690,7 +699,7 @@ function paf_asmstat(args)
if (t[3] - t[2] < min_seg_len) continue;
if (t[0] != last_qname) {
if (last_qname != null)
qcov += process_query(qblocks, qblock_len, bp);
qcov += process_query(qblocks, qblock_len, bp, qinfo[last_qname]);
qblocks = [];
last_qname = t[0];
}
@ -698,7 +707,7 @@ function paf_asmstat(args)
qblocks.push([t[2], t[3], t[4], t[5], t[7], t[8]]);
}
if (last_qname != null)
qcov += process_query(qblocks, qblock_len, bp);
qcov += process_query(qblocks, qblock_len, bp, qinfo[last_qname]);
file.close();
// compute NG50
@ -733,13 +742,32 @@ function paf_asmstat(args)
rst[5][i] = n_breaks;
rst[6][i] = count_bp(bp, 500, 0);
rst[7][i] = count_bp(bp, 500, 10000);
// nb-plot
var qa = [];
for (var qn in qinfo)
qa.push([qinfo[qn].len, qinfo[qn].bp]);
qa = qa.sort(function(a, b) { return b[0] - a[0] });
var sum = 0, n_bp = 0, next_quantile = 0.1;
for (var j = 0; j < qa.length; ++j) {
sum += qa[j][0];
for (var k = 0; k < qa[j][1].length; ++k)
if (qa[j][1][k][0] >= bp_flank_len && qa[j][1][k][1] >= bp_gap_len)
++n_bp;
if (sum >= ref_len * next_quantile) {
print(label, Math.floor(next_quantile * 100 + .5), qa[j][0], (sum / n_bp).toFixed(0), n_bp);
next_quantile += 0.1;
if (next_quantile >= 1.0) break;
}
}
}
print(header.join("\t"));
for (var i = 0; i < labels.length; ++i)
print(labels[i], rst[i].join("\t"));
buf.destroy();
if (bp_flank_len <= 0) {
print(header.join("\t"));
for (var i = 0; i < labels.length; ++i)
print(labels[i], rst[i].join("\t"));
}
}
function paf_stat(args)