I have a fasta file for a virus and generated its annotation with pharokka. The program provided a series of files that include a gff.
I now need to deposit the file to BankIt for insertion into the GenaBank, cut it is needed a sequin file. I tried to convert to TBL3 using gff3-to-tbl, but I got an error:
$ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final_merged_output.tsv .../Consensus/reference.fasta .../Annotation/phanotate.faa > outFile.tbl3
usage: gff3-to-tbl [-h] [--centre CENTRE] [--locustag LOCUSTAG]
project.fsa project.gff product.tsv protein.fa
gff3-to-tbl: error: the following arguments are required: protein.fa
following the guide gff3-to-tbl project.gff product.tsv protein.fa >project.tbl3
.
The files in the Annotation directory were generated by pharokka.
What files from Pharokka do I need to send to get the Sequin file?
Thank you
Thank you, I have updated the title as suggested. But in the command, there a gff, a tsv, and a protein fasta. The list of files is:
I think phanotate.faa is the fasta with the protein translations....
So should your command not be (assuming these are the right files) ?
In case the program is strict about filename extensions you may need to rename
.faa
to.fa
.ADDENDUM: I have seen that pharokka already provides a tbl file; anyway, the question remains: if I needed to convert a gff to sequin with gff3-to-tbl, how would I do that? Thanks