I want gff3 files for certain Vertebrates, but I could only find the corresponding genbank files in Ensembl. So I decided to download them and convert them to gff3, using the bioperl script bp_genbank2gff3. Even though it produces a gff3 file, I get an error and I'm not sure if the resulting file is okay to use... More specifically, the most frequent message I get is a "Possible gene unflattening error".
I have used bp_genbank2gff3 a few times so far, but it's the first time I'm seeing that kind of error. What I find weird is that, even though it says it encountered an error, it produces a gff file...
If you want to reproduce the error, get the following genbank file
wget ftp://ftp.ensembl.org/pub/release-73/genbank/gallus_gallus/Gallus_gallus.Galgal4.73.chromosome.10.dat.gz
and try to convert it using
bp_genkbank2gff3 Gallus_gallus.Galgal4.73.chromosome.10.dat.gz
For your information, I have also tried first decompressing the gzipped file and then running bp_genbank2gff3, but I still get the same error.
Has anyone else seen this error? If so, how do you fix it?
Thanks, Panos
