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convert GTF/GFF3 to BED12

This commit is contained in:
Heng Li 2018-01-05 17:10:43 -05:00
parent 680b971bb0
commit cfe87f50c1
1 changed files with 110 additions and 0 deletions
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110
misc/gff2bed.js 100644
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@ -0,0 +1,110 @@
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;
}
var c;
while ((c = getopt(arguments, "")) != null) {
}
if (getopt.ind == arguments.length) {
print("Usage: k8 gff2bed.js <in.gff>");
exit(1);
}
function print_bed12(exons, cds_st, cds_en)
{
if (exons.length == 0) return;
var name = exons[0].slice(4, 7).join("|");
var a = exons.sort(function(a,b) {return a[1]-b[1]});
var sizes = [], starts = [], st, en;
st = a[0][1];
en = a[a.length - 1][2];
if (cds_st == 1<<30) cds_st = st;
if (cds_en == 0) cds_en = en;
if (cds_st < st || cds_en > en)
throw Error("inconsistent thick start or end for transcript " + a[0][4]);
for (var i = 0; i < a.length; ++i) {
sizes.push(a[i][2] - a[i][1]);
starts.push(a[i][1]);
}
print(a[0][0], st, en, name, 0, a[0][3], cds_st, cds_en, ".", a.length, sizes.join(",") + ",", starts.join(",") + ",");
}
var re_gtf = /(transcript_id|transcript_type|transcript_biotype|gene_name) "([^"]+)";/g;
var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name)=([^;]+)/g;
var buf = new Bytes();
var file = new File(arguments[getopt.ind]);
var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null;
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
if (t[0].charAt(0) == '#') continue;
if (t[2] != "CDS" && t[2] != "exon") continue;
t[3] = parseInt(t[3]) - 1;
t[4] = parseInt(t[4]);
var id = null, type = "", gname = "N/A", biotype = "", m;
while ((m = re_gtf.exec(t[8])) != null) {
if (m[1] == "transcript_id") id = m[2];
else if (m[1] == "transcript_type") type = m[2];
else if (m[1] == "transcript_biotype") biotype = m[2];
else if (m[1] == "gene_name") name = m[2];
}
while ((m = re_gff3.exec(t[8])) != null) {
if (m[1] == "transcript_id") id = m[2];
else if (m[1] == "transcript_type") type = m[2];
else if (m[1] == "transcript_biotype") biotype = m[2];
else if (m[1] == "gene_name") name = m[2];
}
if (type == "" && biotype != "") type = biotype;
if (id == null) throw Error("No transcript_id");
if (id != last_id) {
print_bed12(exons, cds_st, cds_en);
exons = [], cds_st = 1<<30, cds_en = 0;
last_id = id;
}
if (t[2] == "CDS") {
cds_st = cds_st < t[3]? cds_st : t[3];
cds_en = cds_en > t[4]? cds_en : t[4];
} else if (t[2] == "exon") {
exons.push([t[0], t[3], t[4], t[6], id, type, name]);
}
}
if (last_id != null)
print_bed12(exons, cds_st, cds_en);
file.close();
buf.destroy();