Jacques Dainat
There is no such validator. We might implement such tool but as you mentioned other tools exist like `validate_gtf` from the Brent Lab. You might check manually for common mistakes....
I don't get your problem, by default: ``` scaffold625 337817 343277 CLUHART00000008717 0 + 337914 343033 255,0,0 4 154,109,111,1314 0,2915,3700,4146 ``` gives ``` ##gff-version 3 scaffold625 data gene 337818 343277...
Some users experienced the same problem. It occurred for particular GFF formatted files. It has been resolved in more recent version of AGAT. Please update AGAT.
Yes I could add a patch to reformat the Fasta file in such case, but I would prefer that this type of fix is hold within Bioperl directly. If your...
See here for discussion with bioperl team: https://github.com/bioperl/bioperl-live/issues/345
Could you send me over example files providing this error? What AGAT version did you used?
Without your file I cannot help you more. I hope you found your way, don't hesitate to reopen the issue if you are still in trouble.
Hi, Which version of agat were you using? Yes the files would be useful thanks
Humm it sounds I should completely rewrite this script I'm not sure to be able to fix it has it is.
Fixed in AGAT v1.0.0