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slt666666 / NLRtracker

NLR annotation tool
MIT License
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Invalid GFF3 attributes #12

Open darcyabjones opened 2 years ago

darcyabjones commented 2 years ago

Hi there!

Thanks for your great tool and database :) In the GFF3 output the "FIMO" entries contain a keyless value after pvalue=xxxx.

e.g.

seqid   fimo    sequence_motif  198 218 209 +   .   Name=P-loop;Signature=Motif 1;pvalue=1.28e-21;2.41e-15;sequence=PIVGMGGVGKTTLAQSVYNHQ
-------------------------------------------------------------------------------------------------------------------------^^^^^^^^-------------------------------

The value 2.41e-15 needs a key so that GFF3 parsers don't raise errors.

I guess GFF3 isn't the most used output for protein annotation, but we are using them to map the protein coordinates onto the genome so we can look for NLRs near GWAS peaks. It's not too hard to fix on our end, just FYI for any future updates.

Thanks again, Darcy

slt666666 commented 1 year ago

Dear Darcy Thank you for your useful comment! We'll fix this point soon. Many thanks! Toshi