Hello Guys,
I'm having a problem converting a gff3 file format (Augustus output file) in table feature table file (.tbl) to submit contigs in Genbank. Anyone have any script that does it?
Thanks!
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elfeu •
That could be done by using the EMBOSS seqret. Following are few examples:
For EMBL format conversion:
seqret -sequence test.fasta -feature -fformat gff -fopenfile test.gff -osformat embl -auto
For Genbank format conversion:
seqret -sequence test.fasta -feature -fformat gff -fopenfile test.gff -osformat genbank -auto
I hope this would be helpful.
Good luck
This script is generating file which is never finishing and all your hard disc space in finished. I tried it on my pc first and then on external hard disc and 500 gb was not sufficient. :/
I am trying to do this but its not working for me. It says after sometime "Killed: 9" Can you please comment?
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Just be warned that you will still need to do a LOT of work to make the produced .TBL file have valid syntax and semantics for Genbank. It can be an exhausting process. Good luck!
Hi Rahul,
The script you mentioned is producing genbank file format and not .tbl file. Can you please comment on it? Thanks