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option to keep Ensembl_canonical only

This commit is contained in:
Heng Li 2022-05-14 11:18:06 -04:00
parent 31de4fd1bc
commit 50a26a60a6
1 changed files with 11 additions and 7 deletions
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18
misc/paftools.js
View File

@ -1532,22 +1532,24 @@ function paf_view(args)
function paf_gff2bed(args)
{
var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false, output_gene = false;
while ((c = getopt(args, "u:sgjG")) != null) {
var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false, output_gene = false, ens_canon_only = false;
while ((c = getopt(args, "u:sgjGe")) != null) {
if (c == 'u') fn_ucsc_fai = getopt.arg;
else if (c == 's') is_short = true;
else if (c == 'g') keep_gff = true;
else if (c == 'j') print_junc = true;
else if (c == 'G') output_gene = true;
else if (c == 'e') ens_canon_only = true;
}
if (getopt.ind == args.length) {
print("Usage: paftools.js gff2bed [options] <in.gff>");
print("Options:");
print(" -j Output junction BED");
print(" -s Print names in the short form");
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)");
print(" -e only show transcript tagged with 'Ensembl_canonical'");
print(" -g output GFF (used with -u)");
exit(1);
}
@ -1606,7 +1608,7 @@ function paf_gff2bed(args)
print(a[0][0], st, en, name, 1000, a[0][3], cds_st, cds_en, color, a.length, sizes.join(",") + ",", starts.join(",") + ",");
}
var re_gtf = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name) "([^"]+)";/g;
var re_gtf = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name|tag) "([^"]+)";/g;
var re_gff3 = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name)=([^;]+)/g;
var re_gtf_gene = /\b(gene_id|gene_type|gene_name) "([^;]+)";/g;
var re_gff3_gene = /\b(gene_id|gene_type|source_gene|gene_biotype|gene_name)=([^;]+);/g;
@ -1646,13 +1648,14 @@ function paf_gff2bed(args)
if (t[2] != "CDS" && t[2] != "exon") continue;
t[3] = parseInt(t[3]) - 1;
t[4] = parseInt(t[4]);
var id = null, type = "", name = "N/A", biotype = "", m, tname = "N/A";
var id = null, type = "", name = "N/A", biotype = "", m, tname = "N/A", ens_canonical = false;
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" || m[1] == "gbkey") biotype = m[2];
else if (m[1] == "gene_name" || m[1] == "gene_id") name = m[2];
else if (m[1] == "transcript_name") tname = m[2];
else if (m[1] == "tag" && m[2] == "Ensembl_canonical") ens_canonical = true;
}
while ((m = re_gff3.exec(t[8])) != null) {
if (m[1] == "transcript_id") id = m[2];
@ -1661,6 +1664,7 @@ function paf_gff2bed(args)
else if (m[1] == "gene_name" || m[1] == "gene_id") name = m[2];
else if (m[1] == "transcript_name") tname = m[2];
}
if (ens_canon_only && !ens_canonical) continue;
if (type == "" && biotype != "") type = biotype;
if (id == null) throw Error("No transcript_id");
if (id != last_id) {