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more robust ID conversion

This commit is contained in:
Heng Li 2018-01-05 17:55:24 -05:00
parent 209beb9955
commit b20839be77
1 changed files with 8 additions and 4 deletions
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12
misc/gff2bed.js
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@ -53,8 +53,8 @@ if (fn_ucsc_fai != null) {
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
var s = t[0];
if (/_(random|alt)$/.test(s)) {
s = s.replace(/_(random|alt)$/, '');
if (/_(random|alt|decoy)$/.test(s)) {
s = s.replace(/_(random|alt|decoy)$/, '');
s = s.replace(/^chr\S+_/, '');
} else {
s = s.replace(/^chrUn_/, '');
@ -121,8 +121,12 @@ while (file.readline(buf) >= 0) {
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") {
if (fn_ucsc_fai != null && ens2ucsc[t[0]] != null)
t[0] = ens2ucsc[t[0]];
if (fn_ucsc_fai != null) {
if (ens2ucsc[t[0]] != null)
t[0] = ens2ucsc[t[0]];
else if (/^[A-Z]+\d+\.\d+$/.test(t[0]))
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]);
}
}