Unable to extract cds and exons fasta file from exonerate gff file using exonerate-protein2genome-gff-to-fasta.pl

Question

[Junior]

Hey

Can anyone help?

I got this error: Use of uninitialized value $orientation in string eq at exonerate-protein2genome-gff-to-fasta.pl line 90, line 164

Line 164 of my gff: genex xnt2h   CDSpart 5231111 5234643 .       +       .       src=YNT;grp=gene-ara_004913800_1;pri=6

I am wondering why the error occurs

[iraun]

My guess is that the script is not very happy about "CDSpart" annotations. You can try to replace CDSpart by CDS and check if the issue is solved. And then analyze wheter it makes sense to replace CDSpart by CDS or if you should remove CDSpart lines.. etc.