TRANSLOCATION

[pnrobinson]

We should probably support translocation -- the fact that somebody has a clinical picture of disease and a translocation that disrupts the corresponding gene is taken to be evidence that the molecular mechanism of the translocation is an ABLATION of the gene.
In any case, the error message is very alarming:
https://github.com/monarch-initiative/gpsea-cs/blob/develop/notebooks/SATB2/SATB2_gpsea.ipynb
But in practice the user can ignore it in this case -- but people will think it is irrevocably broken.
It would be better to have a message in RED

We removed 6 cases from analysis because the variant type TRANSLOCATION is not supported. 150 cases remain.

[pnrobinson]

This is an example phenopacket from SATB2, PMID_31021519_Case1fromBreweretal.json, it has a translocation and should be included in our GPSEA cohort.

[ielis]

I addressed this in #391. However, I added a new VariantEffect enum member, VariantEffect.TRANSCRIPT_TRANSLOCATION, which corresponds to transcript_translocation SO:0001883.

@pnrobinson pls give this 👍 if it sounds OK.

[pnrobinson]

That is a better SO term than the one I was using in pyphetools, but let us go for it. This meqns we will have to use another version of ppkt store

[ielis]

OK, let's close then.