Since the default representation of genes in Chado is for features to have types gene->mRNA->exon,polypeptide, the default behavior for the Tripal loader should be the same as for the perl loader; that is, when it finds genes that are structured like gene->mRNA->CDS or gene->mRNA->exon,CDS, it should convert them to features that have exons and polypeptides and not load the CDS features. It would be fine with me if this is an option that can be turned off in the Tripal UI though.

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spficklin’s picture

Version: » 7.x-2.x-dev
Component: Code » Documentation
Issue summary: View changes

So, finally getting to this issue. A few questions. Why should CDS features not be loaded? The exon may have be split by a UTR and CDS. Does the perl loader load the UTR and not the CDS? What if we change the loader to behave similarly: create exon and polypeptide sequences, but also load the CDS. Will that cause problems for other tools?

spficklin’s picture

Status: Active » Fixed

Added ability for Tripal GFF3 loader to add protein features if they are absent from the GFF and if the GFF has CDS features. The loader still adds both exon and CDS if both are present. I'm not sure we want to remove the CDS... Need more input on that. So, I'm not closing this, just marking as fixed for now.

spficklin’s picture

Assigned: Unassigned » spficklin
spficklin’s picture

Component: Documentation » Tripal Feature
spficklin’s picture

Status: Fixed » Closed (fixed)

Marking as closed... if problems arise or other comments regarding removing of CDS in favor of exons are added then please reopen.