Output files not always containing CDS filed

[vccarneiro]

Hello,

I was checking the output files because I want to generate a protein fasta in order to run BUSCO. I realized that some files like "combined_with_CDS_high_and_low_confidence_merged.gtf" contain a CDS field for some genes, but for other genes not. Why is that? Exons and CDS coordinates are not always identical. I would appreciate it if you tell me how to obtain the aminoacid sequences corresponding only to CDS coordinates of all genes from the above file. So far, I used the Augustus python script "etAnnoFastaFromJoingenes.py", but it can only extract sequences from .gtf files with annotated CDS coordinates. Any help would be appreciated. Best wishes, Vitor.