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added asmgene 

improvements coming; not made public yet
This commit is contained in:
Heng Li 2018-11-04 17:24:05 -05:00
parent e315b9fada
commit b4ad8d8bf0
1 changed files with 56 additions and 0 deletions
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56
misc/paftools.js
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@ -770,6 +770,61 @@ function paf_asmstat(args)
}
}
function paf_asmgene(args)
{
var c, min_cov = 0.99, min_iden = 0.99;
while ((c = getopt(args, "")) != null);
var n_fn = args.length - getopt.ind;
if (n_fn < 2) {
print("Usage: paftools.js asmgene [options] <ref-splice.paf> <asm-splice.paf> [...]");
exit(1);
}
var buf = new Bytes();
var gene = {}, header = ["Metric"];
for (var i = getopt.ind; i < args.length; ++i) {
var fn = args[i];
var label = fn.replace(/.paf(.gz)?$/, "");
header.push(label);
var file = new File(fn);
var lastq = null;
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
var ql = parseInt(t[1]), qs = parseInt(t[2]), qe = parseInt(t[3]), mlen = parseInt(t[9]), blen = parseInt(t[10]), mapq = parseInt(t[11]);
if (gene[t[0]] == null) {
gene[t[0]] = [];
for (var k = 0; k < n_fn; ++k)
gene[t[0]][k] = 0;
}
if (qe - qs >= ql * min_cov && mlen >= blen * min_iden)
gene[t[0]][i - getopt.ind]++;
}
file.close();
}
var col1 = ["full_uniq", "full_dup", "partial"];
var rst = [];
for (var k = 0; k < col1.length; ++k) {
rst[k] = [];
for (var i = 0; i < n_fn; ++i)
rst[k][i] = 0;
}
for (var g in gene) {
if (gene[g][0] != 1) continue;
for (var i = 0; i < n_fn; ++i) {
if (gene[g][i] == null || gene[g][i] == 0) rst[2][i]++;
else if (gene[g][i] == 1) rst[0][i]++;
else if (gene[g][i] > 1) rst[1][i]++;
}
}
print(header.join("\t"));
for (var k = 0; k < rst.length; ++k) {
print(col1[k], rst[k].join("\t"));
}
buf.destroy();
}
function paf_stat(args)
{
var c, gap_out_len = null;
@ -2238,6 +2293,7 @@ function main(args)
else if (cmd == 'gff2bed') paf_gff2bed(args);
else if (cmd == 'stat') paf_stat(args);
else if (cmd == 'asmstat') paf_asmstat(args);
else if (cmd == 'asmgene') paf_asmgene(args);
else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
else if (cmd == 'call') paf_call(args);
else if (cmd == 'mapeval') paf_mapeval(args);