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bug in block starts; added color and short-name

This commit is contained in:
Heng Li 2018-01-05 21:45:56 -05:00
parent b20839be77
commit a465a920ec
1 changed files with 25 additions and 12 deletions
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37
misc/gff2bed.js
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@ -36,9 +36,10 @@ var getopt = function(args, ostr) {
return optopt; return optopt;
} }
var c, fn_ucsc_fai = null; var c, fn_ucsc_fai = null, is_short = false;
while ((c = getopt(arguments, "u:")) != null) { while ((c = getopt(arguments, "u:s")) != null) {
if (c == 'u') fn_ucsc_fai = getopt.arg; if (c == 'u') fn_ucsc_fai = getopt.arg;
else if (c == 's') is_short = true;
} }
if (getopt.ind == arguments.length) { if (getopt.ind == arguments.length) {
@ -66,10 +67,18 @@ if (fn_ucsc_fai != null) {
buf.destroy(); buf.destroy();
} }
function print_bed12(exons, cds_st, cds_en) var colors = {
'protein_coding':'0,128,255',
'lincRNA':'0,192,0',
'snRNA':'0,192,0',
'miRNA':'0,192,0',
'misc_RNA':'0,192,0'
};
function print_bed12(exons, cds_st, cds_en, is_short)
{ {
if (exons.length == 0) return; if (exons.length == 0) return;
var name = 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]});
var sizes = [], starts = [], st, en; var sizes = [], starts = [], st, en;
st = a[0][1]; st = a[0][1];
@ -80,13 +89,15 @@ function print_bed12(exons, cds_st, cds_en)
throw Error("inconsistent thick start or end for transcript " + a[0][4]); throw Error("inconsistent thick start or end for transcript " + a[0][4]);
for (var i = 0; i < a.length; ++i) { for (var i = 0; i < a.length; ++i) {
sizes.push(a[i][2] - a[i][1]); sizes.push(a[i][2] - a[i][1]);
starts.push(a[i][1]); starts.push(a[i][1] - st);
} }
print(a[0][0], st, en, name, 0, a[0][3], cds_st, cds_en, ".", a.length, sizes.join(",") + ",", starts.join(",") + ","); var color = colors[a[0][5]];
if (color == null) color = '196,196,196';
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 = /(transcript_id|transcript_type|transcript_biotype|gene_name) "([^"]+)";/g; var re_gtf = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name) "([^"]+)";/g;
var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name)=([^;]+)/g; var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name)=([^;]+)/g;
var buf = new Bytes(); var buf = new Bytes();
var file = new File(arguments[getopt.ind]); var file = new File(arguments[getopt.ind]);
@ -97,23 +108,25 @@ while (file.readline(buf) >= 0) {
if (t[2] != "CDS" && t[2] != "exon") continue; if (t[2] != "CDS" && t[2] != "exon") continue;
t[3] = parseInt(t[3]) - 1; t[3] = parseInt(t[3]) - 1;
t[4] = parseInt(t[4]); t[4] = parseInt(t[4]);
var id = null, type = "", gname = "N/A", biotype = "", m; var id = null, type = "", gname = "N/A", biotype = "", m, tname = "N/A";
while ((m = re_gtf.exec(t[8])) != null) { while ((m = re_gtf.exec(t[8])) != null) {
if (m[1] == "transcript_id") id = m[2]; if (m[1] == "transcript_id") id = m[2];
else if (m[1] == "transcript_type") type = m[2]; else if (m[1] == "transcript_type") type = m[2];
else if (m[1] == "transcript_biotype") biotype = m[2]; else if (m[1] == "transcript_biotype") biotype = m[2];
else if (m[1] == "gene_name") name = m[2]; else if (m[1] == "gene_name") name = m[2];
else if (m[1] == "transcript_name") tname = m[2];
} }
while ((m = re_gff3.exec(t[8])) != null) { while ((m = re_gff3.exec(t[8])) != null) {
if (m[1] == "transcript_id") id = m[2]; if (m[1] == "transcript_id") id = m[2];
else if (m[1] == "transcript_type") type = m[2]; else if (m[1] == "transcript_type") type = m[2];
else if (m[1] == "transcript_biotype") biotype = m[2]; else if (m[1] == "transcript_biotype") biotype = m[2];
else if (m[1] == "gene_name") name = m[2]; else if (m[1] == "gene_name") name = m[2];
else if (m[1] == "transcript_name") tname = m[2];
} }
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); print_bed12(exons, cds_st, cds_en, is_short);
exons = [], cds_st = 1<<30, cds_en = 0; exons = [], cds_st = 1<<30, cds_en = 0;
last_id = id; last_id = id;
} }
@ -127,11 +140,11 @@ while (file.readline(buf) >= 0) {
else if (/^[A-Z]+\d+\.\d+$/.test(t[0])) else if (/^[A-Z]+\d+\.\d+$/.test(t[0]))
t[0] = t[0].replace(/([A-Z]+\d+)\.(\d+)/, "chrUn_$1v$2"); t[0] = t[0].replace(/([A-Z]+\d+)\.(\d+)/, "chrUn_$1v$2");
} }
exons.push([t[0], t[3], t[4], t[6], id, type, name]); exons.push([t[0], t[3], t[4], t[6], id, type, name, tname]);
} }
} }
if (last_id != null) if (last_id != null)
print_bed12(exons, cds_st, cds_en); print_bed12(exons, cds_st, cds_en, is_short);
file.close(); file.close();
buf.destroy(); buf.destroy();