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Wild-type genotype edit restriction is unhelpful for PHI-Canto #1842

Closed jseager7 closed 5 years ago

jseager7 commented 5 years ago

(Possibly related: #1244)

@CuzickA is requesting a change to the logic in pathogen–host mode when editing wild-type genotypes. Currently, Canto forbids finishing the edit, and shows a warning:

A wild type allele with wild type product level is only valid in a genotype that has another allele of the same gene.

(See below for a screenshot.)

According to @CuzickA, this isn't ideal for PHI-Canto because "we need to be able to curate wild type control interactions for PHI-base." I don't understand the subtleties here, so this might need some advice from @ValWood or another curator.

Note that there is a workaround that involves using Copy and Edit on the genotype instead, probably to trick Canto into thinking that another allele of the same gene exists, but this definitely isn't intuitive.

The fix might be as simple as disabling the restriction in pathogen–host mode, but I'm not sure since I haven't investigated the code that decides whether the warning should be displayed.

wt_edit_warning

kimrutherford commented 5 years ago

We can add a new option to disable the wildtype expression checking. I'll do that on Monday.

kimrutherford commented 5 years ago

We discussed this issue on yesterday's call. We decided that it would make sense for Alayne and Val to have a chat about this at some point to make sure that this change will allow Alayne to capture the information she needs to.

In the meantime, it was a quick fix so I've gone ahead and added an extra configuration setting that allows the wildtype allele checks to be disabled.

@jseager7 you'll need to add this to the PHI-Canto config file to test the change:

allow_single_wildtype_allele: 1
jseager7 commented 5 years ago

Thanks for this. The change is in production now, and everything works as expected. I'm going to close this issue, because if we decide to refine the restrictions in future that will probably be covered under a new issue.