gffread -w works but not -x and -y

[Ruiqi-CUB]

Hi there, thanks for developing this very useful tool!

I tried to use it to extract CDS and protein from a genome and corresponding gff file.

It works with -w flag and gives me the output. However, it doesn't work with -x or -y flag. Do you happy to know what could cause the issue?

Here is the code I used:
gffread -w(or -x or -y) output.fasta -g genome.fna genome_annot.gff

Thanks a lot

[nian17haoguwen]

Hello, may I ask if this problem you said has been solved? I'm having the same issue.

[Geo Pertea]

I am checking this on the last version but I cannot reproduce the issue it works as expected on the small example files:
gffread -x transcripts_CDS.fa -g genome.fa annotation.gff

gffread -y transcripts_proteins.fa -g genome.fa annotation.gff

Note that these options require the presence of the CDS features in the user provided annotation gff/gtf,