How to convert gff to Sequin format with gff3-to-tbl?

Question

[marongiu.luigi]

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

Answer 1

[GenoMax]

$ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final_merged_output.tsv .../Consensus/reference.fasta .../Annotation/phanotate.faa > outFile.tbl3

Looks like you have an additional entry for the reference fasta file in your command line. Based on the guide you posted above you only need to provide protein fasta.

Also a suggestion for the titles you use for your questions. The title should reflect the problem you are describing in the body of the post. Here you don't need to know How to convert gff to Sequin format? but have a specific problem with gff3-to-tbl script.

[marongiu.luigi]

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:

$ ls *gff
pharokka_aragorn.gff  
pharokka.gff  
pharokka_minced.gff  
trnascan_out.gff
$ ls *tsv
pharokka_cds_final_merged_output.tsv  
pharokka_length_gc_cds_density.tsv
pharokka_cds_functions.tsv            
pharokka_top_hits_mash_inphared.tsv
$ ls *faa
phanotate.faa  
terL.faa

I think phanotate.faa is the fasta with the protein translations....

[GenoMax]

So should your command not be (assuming these are the right files) ?

$ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final_merged_output.tsv  .../Annotation/phanotate.faa > outFile.tbl3

In case the program is strict about filename extensions you may need to rename .faa to .fa.

[marongiu.luigi]

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