Best way to extract gene (CDS) sequences from genome assemblies.

Question

[bioinformaticsscientist]

Hi!

I constantly need to get a comprehensive list of genes for a bacterial/fungal species from an unfinished genome scaffold. What I got from the FTP site are the gff files and the fna files, and I am planning to write a code to extract all genes listed in the gff file from the fna file into a new genes.fsa file. However, before I get down to writing code, I have a feeling that I might be reinventing the wheel. Is there a set-up standard way of going about this? Either a file that I have overlooked that contain the gene-fasta info, or is there a python module that already does this?

Thank you very much!

Answer 1

[Istvan Albert]

bedtools has this covered with the getfasta command.

cufflinks also has the gffread command with similar functionality plus others.