Please apologies if this has been answered somewhere else, but I couldn't find an answer to this problem.
I would like to retrieve all the predicted coding sequences on the NCBI ftp for a given species. Let's say my interest species today is Stegastes partitus and that I go here. I know how to get all the predicted mRNAs (./RNA/Gnomon_mRNA.fsa) or all the predicted proteins (./protein/protein.fa) but I cannot find how to get the CDS... if ever it's possible? This can be done on the Ensembl FTP.
Thanks for any insight!
EDIT: The output would ideally be a multifasta file like this:
>Stegastes_partitus_gene1_cds
ATG(.................................)TAA
>Stegastes_partitus_gene2_cds
ATG(.............................)TGA
>Stegastes_partitus_gene3_cds
...