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A few minor corrections #9
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Without the ID's here we won't be able to keep these two alternative CDS's separate, since they are both in the same mRNA.
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I don't quite understand. The parent mRNAs are different (
mRNA00001,mRNA00002, andmRNA00003).There was a problem hiding this comment.
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Yeah but
cds00003andcds00004both happen to be on the same mRNA in this example (mRNA00003).There was a problem hiding this comment.
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Ah, I see. With
cds00003andcds00004referring to different proteins translated from the same mRNA (different start codons). OK, you're right.The CDS ID should refer to the common ID shared by all genomic intervals in the CDS. This makes sense. So the CDS is considered a discontinuous feature? If this is the right way to do it then pretty much everyone is doing it wrong, giving every CDS row a unique ID.
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Actually in my limited experience (NCBI and Ensembl downloads for human and mouse), they seem to be doing it "right", giving all segments of the discontinuous CDS feature the same ID.
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That's good. Phytozome10, where I get most of my plant genomes, forces unique IDs. Incidentally, I think a group at my university is planning some giant analysis of GFF files, as part of a test of a new domain specific language they are designing. Maybe I can get them look into conventions in the "wild".
But anyway, I agree about the CDS IDs here. I'll push a commit in a bit that reverts the change.
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Since a CDS is discontinuous, are their IDs strictly required, even in mRNAs that contain only a single CDS?
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I'm not sure. Certainly not all CDSs are discontinuous, so I'd guess those would have even less use for an ID. For the discontinuous case I would probably personally still want to see all the chunks having the same ID just for explicitness, but I'm not sure the spec should mandate that.
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So perhaps CDS IDs should be strictly required only when multiple CDS share one mRNA.
When CDS IDs are used, should it be strictly required that each interval in the CDS share the same ID? For example, is this incorrect:
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My fantasy: a registry of all GFF3 files in the wild (or at least a start with a representative sample), and a Jenkins or other CI job that regularly runs a GFF3 validator and reports variations from normative standard and de-facto conventions....
@nathandunn how hard would this be?