Retrieve all predicted cds from NCBI
The GNOMON and GFF folder contains the files you want, the GNOMON if you check the README relates to the GNOMON gene predictor and the GFF I think links back to the same file. I think the file you want is ref_Stegastes_partitus-1.0.2_scaffolds.gff3.gz which contains the coordinates on the scaffolds.

And as you stated you are on linux, so the best and geeky way to go is awk.

awk '!/#/{if($3=="CDS")print}' ref_Stegastes_partitus-1.0.2_scaffolds.gff3 &gt; SomeFile.gff3


UPDATE



This part is from python. With reference to the previous user's answer if you fetch the GBK file, rna.gbk, this should allow you to fetch CDS using biopython

You should also check out Peter cook's tutorial on handling genbank files in python

from Bio import SeqIO
from __future__ import print_function

Genome = SeqIO.parse("Examples/rna.gbk","genbank")
handle = open("Examples/rna.faa","w")
for genes in Genome:
    i=1
    for Feature in genes.features:
        if Feature.type=="CDS":
            FASTA=Feature.extract(genes.seq)
            print("&gt;"+genes.id+"_CDS_"+str(i),file=handle)
            print(FASTA,file=handle) 
            i += 1


I would recommend that you install anaconda, it is a package management software, which when installed installs its own python version and alongside it installs some 400 different packages. Instructions are available on the link. So these packages should come with the link.

After you have installed anaconda, put all that code from up there into a Myfile.py and execute on the command line with python Myfile.py.