search

monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
4 stars 1 forks source link

Buffer vv response #155

Closed pnrobinson closed 1 month ago

pnrobinson commented 1 month ago

I made some changes in the variant drawing code because of None-pointer errors, e.g., 

     variant_locations = list()
      for ann in tx_anns:
          if ann is not None and hasattr(ann, 'protein_effect_location'):
              prot_eff_loc = ann.protein_effect_location
              if prot_eff_loc is not None:
                  variant_locations.append([prot_eff_loc.start, prot_eff_loc.end])
      variant_locations = np.array(variant_locations)
      #variant_locations = np.array([[
      #    ann.protein_effect_location.start,
      #    ann.protein_effect_location.end]
      #    for ann in tx_anns if ann is not None and hasattr(ann, 'protein_effect_location')
      #])

This solved that problem, but I am seeing strange behaviour Screenshot 2024-05-08 at 16 02 03

I am not sure if the problem is related.

pnrobinson commented 1 month ago

crap, I think this PR included changes from another PR -- it is really just the change in the code that is above comment, please delete this PR and just adopt the change if it is correct

ielis commented 1 month ago

crap, I think this PR included changes from another PR -- it is really just the change in the code that is above comment, please delete this PR and just adopt the change if it is correct

yes, it looks like the changes from another PR include deleting some phenopackets. I see 328 KBG phenopackets gone on my diff. I think we should wait until KBG PR is merged and then we should be able to merge this one.