Transfer annotation from fasta headers to associated gff

Question

[EJB]

Hi Everyone,

I have a .fasta file with functional and GO annotations. I also have an associated GFF3 file with the locations of these genes in the genome. The IDs from the GFF3 and fasta match. I need to append the annotation information from the fasta header to the notes column of the appropriate lines in the GFF3 file. something like this:

Fasta Headers:

>evm.model.Scaffold_003599.4 Protein=Olfactory_receptor GO=GO:0004930,...

Current GFF3:

Scaffold_003599 EVM mRNA 187035 187979 . + . ID=evm.model.Scaffold_003599.4

Desired GFF3:

Scaffold_003599   EVM   mRNA   187035   187979 . + .  ID=evm.model.Scaffold_003599.4 Protein=Olfactory_receptor GO=GO:0004930,

Basically, I need to replace each

ID=... (in the gff)

with

ID=... Protein=... GO=... (from the fasta headers)

I feel like this should not be that difficult a task, but it is just out of my range of scripting skills at the moment (or it would take me a long time to figure out how to do this by trial and error).

Does anyone know of a current tool or script to accomplish this?

Thanks!

[Zhilong Jia]

reference this post .

Answer 1

[Juke34]

You can lift this information with agat_sq_add_attributes_from_tsv.pl from AGAT using a csv/tsv file with feature identifier (e.g. gene ID or mRNA ID) in their first column. Invoke the help of this tool for more information.