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compatibility with GenBank GTP (resolves $422)

This commit is contained in:
Heng Li 2019-06-11 09:16:03 -04:00
parent 03dc8d5d97
commit 58c2251b18
1 changed files with 9 additions and 8 deletions
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17
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.17-r941'; var paftools_version = '2.17-r949-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -1509,6 +1509,7 @@ function paf_gff2bed(args)
var colors = { var colors = {
'protein_coding':'0,128,255', 'protein_coding':'0,128,255',
'mRNA':'0,128,255',
'lincRNA':'0,192,0', 'lincRNA':'0,192,0',
'snRNA':'0,192,0', 'snRNA':'0,192,0',
'miRNA':'0,192,0', 'miRNA':'0,192,0',
@ -1541,8 +1542,8 @@ 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(",") + ","); 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|transcript_name) "([^"]+)";/g; var re_gtf = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name) "([^"]+)";/g;
var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name)=([^;]+)/g; var re_gff3 = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name)=([^;]+)/g;
var buf = new Bytes(); var buf = new Bytes();
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]); var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
@ -1559,19 +1560,19 @@ function paf_gff2bed(args)
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, tname = "N/A"; var id = null, type = "", name = "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" || m[1] == "gbkey") biotype = m[2];
else if (m[1] == "gene_name") name = 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] == "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" || m[1] == "gbkey") biotype = m[2];
else if (m[1] == "gene_name") name = 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] == "transcript_name") tname = m[2];
} }
if (type == "" && biotype != "") type = biotype; if (type == "" && biotype != "") type = biotype;