monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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Create a predicate that tests if a variant affects a Region given by the User. #174

Closed lnrekerle closed 1 week ago

lnrekerle commented 2 weeks ago

Rather than only allowing users to pick a specific domain, create a predicate that will allow a user to give a region of amino acids on the protein and look for whether a variant affects an amino acid in that region.

Make sure there is a matching predicate for comparing two regions and for comparing a recessive variant.

pnrobinson commented 1 week ago

@lnrekerle Thanks! One nice way of doing issues like this is to also write something like this "This issue is closeable if a unit test is passed in which the predicate returns true for a region within the indicated range and false for other regions. Document to do about edge conditions -- here, we will consider if the user has a range of 40-80 that a mutation that affects amino acid 40 or 80 is "inside" and that "outside" begins at residues 39 and 81. Have tests for the edge conditions.

pnrobinson commented 1 week ago

This means that a reviewer can run the tests and check that your code does what it is supposed to do, which should make the whole process go more quickly.