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The gff-version listed by helixer is "3.2.1" I haven't been able to find a specification for that version. The only particularly well detailed specification of gff3 that I've ever found is from Sequence Ontology for "3.1.26"...
...According to this standard, CDS lines that are meant to be part of the same sequence should have the same ID. This marks those lines as a multi-line feature. Helixer doesn't do this. Helixer marks each CDS segment with its own ID.
Is there an actual specification for 3.2.1 somewhere? If so, does it disagree with 3.1.26 in terms of how CDS are supposed to be represented?
EDIT: For reference, current GFF from helixer looks like...
I know the difference seems small, but its the difference between a "correct" parsing of the file producing two distinct proteins and producing a single (correct) protein.
The text was updated successfully, but these errors were encountered:
Ah, thanks for raising this. That will help us get it patched up the next round of changes / next version.
As a practical option until then, many parsers use the Parent feature to determine what belongs together and will parse this correctly despite the IDs. I think gffread should do it.
The gff-version listed by helixer is "3.2.1" I haven't been able to find a specification for that version. The only particularly well detailed specification of gff3 that I've ever found is from Sequence Ontology for "3.1.26"...
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
...According to this standard, CDS lines that are meant to be part of the same sequence should have the same ID. This marks those lines as a multi-line feature. Helixer doesn't do this. Helixer marks each CDS segment with its own ID.
Is there an actual specification for 3.2.1 somewhere? If so, does it disagree with 3.1.26 in terms of how CDS are supposed to be represented?
EDIT: For reference, current GFF from helixer looks like...
...According to the sequence ontology standard, it should be...
I know the difference seems small, but its the difference between a "correct" parsing of the file producing two distinct proteins and producing a single (correct) protein.
The text was updated successfully, but these errors were encountered: