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gff2bed to output junction BED

This commit is contained in:
Heng Li 2019-04-27 22:15:40 -04:00
parent 6420acca6d
commit cdc730d573
1 changed files with 18 additions and 7 deletions
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25
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.16-r922'; var paftools_version = '2.16-dirty-r928';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -1469,15 +1469,21 @@ function paf_view(args)
function paf_gff2bed(args) function paf_gff2bed(args)
{ {
var c, fn_ucsc_fai = null, is_short = false, keep_gff = false; var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false;
while ((c = getopt(args, "u:sg")) != null) { while ((c = getopt(args, "u:sgj")) != null) {
if (c == 'u') fn_ucsc_fai = getopt.arg; if (c == 'u') fn_ucsc_fai = getopt.arg;
else if (c == 's') is_short = true; else if (c == 's') is_short = true;
else if (c == 'g') keep_gff = true; else if (c == 'g') keep_gff = true;
else if (c == 'j') print_junc = true;
} }
if (getopt.ind == args.length) { if (getopt.ind == args.length) {
print("Usage: paftools.js gff2bed [-g] [-u ucsc-genome.fa.fai] <in.gff>"); print("Usage: paftools.js gff2bed [options] <in.gff>");
print("Options:");
print(" -j Output junction BED");
print(" -s Print names in the short form");
print(" -u FILE hg38.fa.fai for chr name conversion");
print(" -g Output GFF (used with -u)");
exit(1); exit(1);
} }
@ -1509,11 +1515,16 @@ function paf_gff2bed(args)
'misc_RNA':'0,192,0' 'misc_RNA':'0,192,0'
}; };
function print_bed12(exons, cds_st, cds_en, is_short) function print_bed12(exons, cds_st, cds_en, is_short, print_junc)
{ {
if (exons.length == 0) return; if (exons.length == 0) return;
var name = is_short? exons[0][7] + "|" + exons[0][5] : exons[0].slice(4, 7).join("|"); var name = is_short? exons[0][7] + "|" + exons[0][5] : exons[0].slice(4, 7).join("|");
var a = exons.sort(function(a,b) {return a[1]-b[1]}); var a = exons.sort(function(a,b) {return a[1]-b[1]});
if (print_junc) {
for (var i = 1; i < a.length; ++i)
print(a[i][0], a[i-1][2], a[i][1], name, 1000, a[i][3]);
return;
}
var sizes = [], starts = [], st, en; var sizes = [], starts = [], st, en;
st = a[0][1]; st = a[0][1];
en = a[a.length - 1][2]; en = a[a.length - 1][2];
@ -1566,7 +1577,7 @@ function paf_gff2bed(args)
if (type == "" && biotype != "") type = biotype; if (type == "" && biotype != "") type = biotype;
if (id == null) throw Error("No transcript_id"); if (id == null) throw Error("No transcript_id");
if (id != last_id) { if (id != last_id) {
print_bed12(exons, cds_st, cds_en, is_short); print_bed12(exons, cds_st, cds_en, is_short, print_junc);
exons = [], cds_st = 1<<30, cds_en = 0; exons = [], cds_st = 1<<30, cds_en = 0;
last_id = id; last_id = id;
} }
@ -1584,7 +1595,7 @@ function paf_gff2bed(args)
} }
} }
if (last_id != null) if (last_id != null)
print_bed12(exons, cds_st, cds_en, is_short); print_bed12(exons, cds_st, cds_en, is_short, print_junc);
file.close(); file.close();
buf.destroy(); buf.destroy();