Information request on --forcegene option of v-annotate.pl

[FTouzain]

Hello,
Thank you again for vadr tool.

I created a Porcine Circo Virus databank with types 1, 2, 3 and 4 to do vadr annotations.
Vadr is working fine, but I don't get any "gene" mention, even when I use --forcegene option of v-annotate.pl.

My command line is:

v-annotate.pl --mkey pcv --mdir /db_path/vadr_db/vadr-models-pcv/  --glsearch --split -f --forcegene --cpu 4 pcv2/ref_std/ref_pcv2.fasta pcv2/vadr_outdir/

For instance, I get:

>Feature KT719404.1
51	995	CDS
			product	replicase
			protein_id	KT719404.1_1
671	357	CDS
			product	ORF3 protein
			protein_id	KT719404.1_2
1734	1033	CDS
			product	capsid protein
			protein_id	KT719404.1_3

Is it normal ? Must it be in the original ref annotation to be used in vadr? I was expecting a "gene" line before each CDS (because I parse annotations).

Are you interested in a pcv databank?

Thank you for your clarifications

[nawrockie]

@FTouzain : yes, the gene features must be in the GenBank annotation that the model was built from. If they are not, you can manually add them to the .vadr.minfo output file from v-build.pl. You can just copy the CDS features and edit as necessary. You'll want the value for the gene: key to be the same as the gene: value for the corresponding CDS. This file shows some examples: https://bitbucket.org/nawrockie/vadr-models-sarscov2/src/master/sarscov2.minfo. For example, see lines 9 and 10, which contain the CDS and gene feature information for the E gene.

If you have further questions and share your .minfo files, I can show you what changes to make.