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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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EC_number is an invalid GFF3 attribute key #443

Open standage opened 4 years ago

standage commented 4 years ago

The GFF3 specification states:

All attributes that begin with an uppercase letter are reserved for later use. Attributes that begin with a lowercase letter can be used freely by applications.

"Reserved for later use" is generally interpreted to mean they can only be defined by the official spec. Indeed, when I sort and tidy Prokka output with gt gff3, I get a bunch of the following error messages.

warning: illegal uppercase attribute "EC_number" on line 83 in file "prokka-outdir/prokka.gff"; change to lower case

GenomeTools converts the attribute key from EC_number to eC_number.

tseemann commented 4 years ago

Yes, I violate the GFF3 spec for compatibility with INSDC feature tag standard: http://www.insdc.org/documents/feature_table.html I'm not sure what the best approach is. I have other logic in the code to ensure EC_number is maintained too.

You can do this in your pipeline if needed sed 's/EC_number/ec_number/g' < broken.gff > fixed.gff