convert gtf to gff3

[nextgenusfs]

Tried to convert a non coding RNA GTF file and failed with:

Traceback (most recent call last):
  File "/bioinfo/apps/all_apps/miniconda3/envs/gtools/bin/gfftk", line 8, in <module>
    sys.exit(main())
  File "/bioinfo/apps/all_apps/miniconda3/envs/gtools/lib/python3.6/site-packages/gfftk/__main__.py", line 22, in main
    convert(args)
  File "/bioinfo/apps/all_apps/miniconda3/envs/gtools/lib/python3.6/site-packages/gfftk/convert.py", line 140, in convert
    debug=args.debug,
  File "/bioinfo/apps/all_apps/miniconda3/envs/gtools/lib/python3.6/site-packages/gfftk/convert.py", line 577, in gtf2gff
    dict2gff3(Genes, output=output)
  File "/bioinfo/apps/all_apps/miniconda3/envs/gtools/lib/python3.6/site-packages/gfftk/gff.py", line 2495, in dict2gff3
    if len(v["go_terms"][i]) > 0:
IndexError: list index out of range

So need to check the dictionary being constructed with GTF and/or put a try/except on the extra annotations....

[YingChen94]

Hello, I got the same error. Is there a way to fix it? Thanks!

[nextgenusfs]

Possibly, what does your GTF file look like and where is it from?

[YingChen94]

The gtf file is the output from BRAKER3 annotation pipeline. The first 10 lines look like this:

chr1	GeneMark.hmm3	gene	63	31891	.	-	.	g1
chr1	GeneMark.hmm3	transcript	63	31891	.	-	.	g1.t1
chr1	GeneMark.hmm3	stop_codon	63	65	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	CDS	63	239	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	exon	63	239	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	mRNA	63	31891	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	intron	240	320	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	CDS	321	529	.	-	2	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	exon	321	529	.	-	2	transcript_id "g1.t1"; gene_id "g1";
chr1	GeneMark.hmm3	intron	530	1730	.	-	1	transcript_id "g1.t1"; gene_id "g1";

I found the solution here: Gaius-Augustus/BRAKER#640. Thank you for your help!