Retrieve all predicted cds from NCBI

Question

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!

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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
...

Answer 1

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 > SomeFile.gff3

UPDATE

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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(">"+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.

Answer 2

The RNA folder of your link provides several annotated file formats. These include reference to the CDS for every transcript.

Stegastes_partitus/RNA/

Download and unzip the rna.gbk.gz file and open it. You will see CDS location information for every entry.

Answer 3

A web-based way of getting this data:

1. Go to the NCBI Assembly page: https://www.ncbi.nlm.nih.gov/assembly and search for the species of your interest. Here, the query would be something like "Stegastes partitus"[Organism] which would return only one hit that is the latest reference version of the assembly. Since there is only one hit, you are directed to the 'Full Report' page by default. Click on the link at the top left corner and change the 'Full Report' format to 'Summary'
2. At this point, you will see a 'Download Assemblies' button. Click on that, choose the data source as RefSeq and file type as 'CDS from genomic' and you are good to go!