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added paf2gff

This commit is contained in:
Heng Li 2022-09-08 22:33:21 -04:00
parent 15cade0f06
commit e450f161bb
1 changed files with 75 additions and 0 deletions
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75
misc/paftools.js
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@ -3149,6 +3149,79 @@ function paf_longcs2seq(args) {
buf.destroy();
}
function paf_paf2gff(args) {
var c, opt = { aa:false };
var re_cigar = /(\d+)([A-Z=])/g;
while ((c = getopt(args, "a")) != null) {
if (c == 'a') opt.aa = true;
}
if (args.length == getopt.ind) {
print("Usage: paftools.js paf2gff [-a] <in.paf>");
return;
}
var buf = new Bytes();
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
var hid = 1, last_name = null;
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0] != last_name) last_name = t[0], hid = 1;
else ++hid;
for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]);
for (var i = 6; i <= 11; ++i) t[i] = parseInt(t[i]);
var cigar = null, score = null;
for (var i = 12; i < t.length; ++i) {
if ((m = /^(cg:Z|AS:i):(\S+)/.exec(t[i])) != null) {
if (m[1] == 'cg:Z') cigar = m[2];
else if (m[1] == 'AS:i') score = parseInt(m[2]);
}
}
if (cigar == null) throw Error("failed to find the cg:Z tag");
if (score == null) throw Error("failed to find the AS:i tag");
var st = 0, en = 0, phase = 0, pseudo = false, fs = 0, a = [];
while ((m = re_cigar.exec(cigar)) != null) {
var len = parseInt(m[1]);
if (m[2] == 'M' || m[2] == 'D') {
en += opt.aa? len * 3 : len;
} else if (m[2] == 'F' || m[2] == 'G' || m[2] == 'R') {
en += len, pseudo = true, fs = 1;
} else if (m[2] == 'N') {
a.push([t[5], 'paf2gff', 'exon', st, en, 0, t[4], phase, fs]);
st = en + len, en += len, phase = 0, fs = 0;
} else if (m[2] == 'U') { // ...xGT...AGxx...
a.push([t[5], 'paf2gff', 'exon', st, en + 1, 0, t[4], phase, fs]);
st = en + len - 2, en += len, phase = 2, fs = 0;
} else if (m[2] == 'V') { // ...xxGT...AGx...
a.push([t[5], 'paf2gff', 'exon', st, en + 2, 0, t[4], phase, fs]);
st = en + len - 1, en += len, phase = 1, fs = 0;
}
}
a.push([t[5], 'paf2gff', 'exon', st, en, 0, t[4], phase, fs]);
if (en != t[8] - t[7]) throw Error("inconsistent cigar");
var type = pseudo? 'pseudogene' : 'protein_coding';
var attr = ['transcript_id=' + t[0] + '#' + hid, 'transcript_type=' + type].join(";");
print([t[5], 'paf2gff', 'transcript', t[7] + 1, t[8], score, t[4], '.', attr].join("\t"));
if (opt.aa && t[4] == '-') {
var b = [], len = t[8] - t[7];
for (var i = a.length - 1; i >= 0; --i) {
var x = len - a[i][3];
a[i][3] = len - a[i][4];
a[i][4] = x;
//a[i][7] = a[i][7] == 0? 0 : 3 - a[i][7]; // not sure if this line is needed
b.push(a[i]);
}
a = b;
}
for (var i = 0; i < a.length; ++i) {
a[i][3] += t[7] + 1;
a[i][4] += t[7];
a[i][8] = attr + ";frameshift=" + a[i][8];
print(a[i].join("\t"));
}
}
file.close();
buf.destroy();
}
/*************************
***** main function *****
*************************/
@ -3164,6 +3237,7 @@ function main(args)
print(" delta2paf convert MUMmer's delta to PAF");
print(" gff2bed convert GTF/GFF3 to BED12");
print(" longcs2seq convert long-cs PAF to sequences");
print(" paf2gff convert PAF to GFF3 (tested for miniprot only)");
print("");
print(" stat collect basic mapping information in PAF/SAM");
print(" asmstat collect basic assembly information");
@ -3209,6 +3283,7 @@ function main(args)
else if (cmd == 'sveval') paf_sveval(args);
else if (cmd == 'vcfsel') paf_vcfsel(args);
else if (cmd == 'longcs2seq') paf_longcs2seq(args);
else if (cmd == 'paf2gff') paf_paf2gff(args);
else if (cmd == 'version') print(paftools_version);
else throw Error("unrecognized command: " + cmd);
}