How to get CDS.fasta from gff file + sequenceFile.fasta

Question

[moranr]

I have two files:

1. An annotation file in gff format
2. A fasta formatted sequnce file for a whole genome.

I want to have a resulting file : myGenomeCDS.fasta

How can I go about doing this via python or Tools ?

Thanks

Answer 1

[iraun]

If your gtf file has the annotation of CDS's you can extract CDS sequences using gffread in this way:

gffread -g genome.fa -x CDS.fa annotation.gtf

Answer 2

[arnstrm]

There are so many ways to do this. If you don't want to write your own code, use the utilities from preexisiting packages such as BedTools (fastafrombed), Glimmer (extract) and even Galaxy as a tool (extract features).