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  1. #!/usr/bin/awk -f
  2. BEGIN {
  3.   FS=OFS="\t"
  4. }
  5. {
  6.   gsub(/; *$/, "", $9)        # trim trailing `;'
  7.   split($9, pairs, / *; */)   # split attributes into pairs
  8.   for (i in pairs) {
  9.     split(pairs[i], kv, / */) # split pair into key and value
  10.     attr[kv[1]] = kv[2]       # add it to `attr'
  11.   }
  12.   # fill missing fields
  13.   if (!("gene_name" in attr))
  14.     attr["gene_name"] = attr["gene_id"]
  15.   if (!("transcript_id" in attr))
  16.     attr["transcript_id"] = attr["gene_id"]
  17.   if (!("transcript_name" in attr))
  18.     attr["transcript_name"] = attr["transcript_id"];
  19.   # recreate the attributes field
  20.   attr_all = sep = ""
  21.   for (k in attr) {
  22.     attr_all = attr_all sep k " " attr[k]
  23.     sep = "; "
  24.   }
  25.   # update the record with new attributes
  26.   $9 = attr_all 
  27. }
  28. 1 # print record
Success #stdin #stdout 0s 7376KB
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stdin
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1	ensembl	gene	5273	10061	.	-	.	gene_id ENSGALG00000054818; gene_version 1; gene_source ensembl; gene_biotype protein_coding;
1	ensembl	transcript	5273	10061	.	-	.	gene_id ENSGALG00000054818; gene_version 1; transcript_id ENSGALT00000098984; transcript_version 1; gene_source ensembl; gene_biotype protein_coding; transcript_source ensembl; transcript_biotype protein_coding;
1	ensembl	gene	58427	58617	.	+	.	gene_id ENSGALG00000047594; gene_version 1; gene_name RF00004; gene_source ensembl; gene_biotype snRNA;
1	ensembl	transcript	58427	58617	.	+	.	gene_id ENSGALG00000047594; gene_version 1; transcript_id ENSGALT00000094382; transcript_version 1; gene_name RF00004; gene_source ensembl; gene_biotype snRNA; transcript_name RF00004-201; transcript_source ensembl; transcript_biotype snRNA;
1	ensembl	exon	58427	58617	.	+	.	gene_id ENSGALG00000047594; gene_version 1; transcript_id ENSGALT00000094382; transcript_version 1; exon_number 1; gene_name RF00004; gene_source ensembl; gene_biotype snRNA; transcript_name RF00004-201; transcript_source ensembl; transcript_biotype snRNA; exon_id ENSGALE00000460125; exon_version 1;
1	ensembl	gene	63264	63454	.	+	.	gene_id ENSGALG00000049206; gene_version 1; gene_name RF00004; gene_source ensembl; gene_biotype snRNA;
1	ensembl	transcript	63264	63454	.	+	.	gene_id ENSGALG00000049206; gene_version 1; transcript_id ENSGALT00000092780; transcript_version 1; gene_name RF00004; gene_source ensembl; gene_biotype snRNA; transcript_name RF00004-201; transcript_source ensembl; transcript_biotype snRNA;
1	ensembl	exon	63264	63454	.	+	.	gene_id ENSGALG00000049206; gene_version 1; transcript_id ENSGALT00000092780; transcript_version 1; exon_number 1; gene_name RF00004; gene_source ensembl; gene_biotype snRNA; transcript_name RF00004-201; transcript_source ensembl; transcript_biotype snRNA; exon_id ENSGALE00000501941; exon_version 1;
stdout
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1	ensembl	gene	5273	10061	.	-	.	transcript_name ENSGALG00000054818; transcript_id ENSGALG00000054818; gene_name ENSGALG00000054818; gene_id ENSGALG00000054818; gene_source ensembl; gene_biotype protein_coding; gene_version 1
1	ensembl	transcript	5273	10061	.	-	.	transcript_name ENSGALG00000054818; transcript_id ENSGALT00000098984; transcript_source ensembl; gene_name ENSGALG00000054818; transcript_biotype protein_coding; gene_id ENSGALG00000054818; transcript_version 1; gene_source ensembl; gene_biotype protein_coding; gene_version 1
1	ensembl	gene	58427	58617	.	+	.	transcript_name ENSGALG00000054818; transcript_id ENSGALT00000098984; transcript_source ensembl; gene_name RF00004; transcript_biotype protein_coding; gene_id ENSGALG00000047594; transcript_version 1; gene_source ensembl; gene_biotype snRNA; gene_version 1
1	ensembl	transcript	58427	58617	.	+	.	transcript_name RF00004-201; transcript_id ENSGALT00000094382; transcript_source ensembl; gene_name RF00004; transcript_biotype snRNA; gene_id ENSGALG00000047594; transcript_version 1; gene_source ensembl; gene_biotype snRNA; gene_version 1
1	ensembl	exon	58427	58617	.	+	.	transcript_name RF00004-201; transcript_id ENSGALT00000094382; transcript_source ensembl; gene_name RF00004; transcript_biotype snRNA; gene_id ENSGALG00000047594; transcript_version 1; exon_version 1; gene_source ensembl; gene_biotype snRNA; exon_number 1; gene_version 1; exon_id ENSGALE00000460125
1	ensembl	gene	63264	63454	.	+	.	transcript_name RF00004-201; transcript_id ENSGALT00000094382; transcript_source ensembl; gene_name RF00004; transcript_biotype snRNA; gene_id ENSGALG00000049206; transcript_version 1; exon_version 1; gene_source ensembl; gene_biotype snRNA; exon_number 1; gene_version 1; exon_id ENSGALE00000460125
1	ensembl	transcript	63264	63454	.	+	.	transcript_name RF00004-201; transcript_id ENSGALT00000092780; transcript_source ensembl; gene_name RF00004; transcript_biotype snRNA; gene_id ENSGALG00000049206; transcript_version 1; exon_version 1; gene_source ensembl; gene_biotype snRNA; exon_number 1; gene_version 1; exon_id ENSGALE00000460125
1	ensembl	exon	63264	63454	.	+	.	transcript_name RF00004-201; transcript_id ENSGALT00000092780; transcript_source ensembl; gene_name RF00004; transcript_biotype snRNA; gene_id ENSGALG00000049206; transcript_version 1; exon_version 1; gene_source ensembl; gene_biotype snRNA; exon_number 1; gene_version 1; exon_id ENSGALE00000501941
https://ideone.com/vDFpqk
language:
AWK (mawk 1.3.3)
created:
6 years ago
visibility:
public

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