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extract junctions from GFF

This commit is contained in:
Heng Li 2022-09-21 12:57:40 -04:00
parent 6ed7263670
commit 5aa4355ca8
1 changed files with 44 additions and 1 deletions
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45
misc/paftools.js
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@ -3283,6 +3283,47 @@ function paf_paf2gff(args) {
buf.destroy();
}
function paf_gff2junc(args) {
var c, feat = "CDS";
while ((c = getopt(args, "f:")) != null) {
if (c == 'f') feat = getopt.arg;
}
if (getopt.ind == args.length) {
print("Usage: paftools.js gff2junc [-f feature] <in.gff3>");
return;
}
var buf = new Bytes();
var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
function process_a(a) {
if (a.length < 2) return;
a = a.sort(function(x, y) { return x[4] - y[4] });
for (var i = 1; i < a.length; ++i)
print([a[i][1], a[i-1][5], a[i][4], a[i][0], 0, a[i][7]].join("\t"));
}
var a = [];
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0][0] == '#') continue;
if (t[2].toLowerCase() != feat.toLowerCase()) continue;
//print(t.join("\t"));
if ((m = /\bParent=([^;]+)/.exec(t[8])) == null)
throw Error("Can't find Parent");
t[3] = parseInt(t[3]) - 1;
t[4] = parseInt(t[4]);
t.unshift(m[1]);
if (a.length > 0 && a[0][0] != m[1]) {
process_a(a);
a.length = 0;
a.push(t);
} else a.push(t);
}
process_a(a);
file.close();
buf.destroy();
}
/*************************
***** main function *****
*************************/
@ -3297,8 +3338,9 @@ function main(args)
print(" sam2paf convert SAM to PAF");
print(" delta2paf convert MUMmer's delta to PAF");
print(" gff2bed convert GTF/GFF3 to BED12");
print(" gff2junc convert GFF3 to junction BED");
print(" longcs2seq convert long-cs PAF to sequences");
print(" paf2gff convert PAF to GFF3 (tested for miniprot only)");
// 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");
@ -3326,6 +3368,7 @@ function main(args)
else if (cmd == 'delta2paf') paf_delta2paf(args);
else if (cmd == 'splice2bed') paf_splice2bed(args);
else if (cmd == 'gff2bed') paf_gff2bed(args);
else if (cmd == 'gff2junc') paf_gff2junc(args);
else if (cmd == 'stat') paf_stat(args);
else if (cmd == 'asmstat') paf_asmstat(args);
else if (cmd == 'asmgene') paf_asmgene(args);