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r754: option to only change name

This commit is contained in:
Heng Li 2018-03-23 12:27:11 -04:00
parent 5ef9580b17
commit 1c504d72e4
1 changed files with 11 additions and 4 deletions
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15
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = 'r746'; var paftools_version = 'r754';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -993,14 +993,15 @@ function paf_view(args)
function paf_gff2bed(args) function paf_gff2bed(args)
{ {
var c, fn_ucsc_fai = null, is_short = false; var c, fn_ucsc_fai = null, is_short = false, keep_gff = false;
while ((c = getopt(args, "u:s")) != null) { while ((c = getopt(args, "u:sg")) != 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;
} }
if (getopt.ind == args.length) { if (getopt.ind == args.length) {
print("Usage: paftools.js gff2bed [-u ucsc-genome.fa.fai] <in.gff>"); print("Usage: paftools.js gff2bed [-g] [-u ucsc-genome.fa.fai] <in.gff>");
exit(1); exit(1);
} }
@ -1061,6 +1062,12 @@ function paf_gff2bed(args)
var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null; var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null;
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t"); var t = buf.toString().split("\t");
if (keep_gff) {
if (t[0].charAt(0) != '#' && ens2ucsc[t[0]] != null)
t[0] = ens2ucsc[t[0]];
print(t.join("\t"));
continue;
}
if (t[0].charAt(0) == '#') continue; if (t[0].charAt(0) == '#') continue;
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;