Closed KaparaNewbie closed 1 year ago
@MillironX, could you kindly review this?
Thank you, @MillironX, for your very kind response. I think I addressed all your points (hopefully there are enough tests).
Base: 88.20% // Head: 88.28% // Increases project coverage by +0.08%
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Sounds good, thanks.
Sorry about the .gitignore
thing. My git skill is (still) embarrassingly noobish.
Add support for R. Grantham's substitution matrix from his 1974 paper
Types of changes
:clipboard: Additional detail
If you have implemented new features or behaviour
Description of the addition This PR adds support for R. Grantham's substitution matrix from his 1974 paper in which the distance between any two amino acids is based on three physicochemical properties: composition, polarity, and molecular volume.
In addition,
default_match=0, default_mismatch=0
are kwargs in theload_submat
andparse_ncbi_submat
functions. Existing calls to PAM and BLOSUM aren't changed as a result. For the newGRANTHAM1974
matrix, I chosedefault_mismatch = 100
because 100 is the mean value in Grantham's original table.Justification of the addition Two justifications should be provided: (a) for the addition of the matrix, (b) and the (unbreaking!) changes to the
load_submat
andparse_ncbi_submat
functions.default_mismatch
compared todefault_mismatch == 0
as in the original return valueSubstitutionMatrix(scores, default_match=0, default_mismatch=0)
in the final line of theparse_ncbi_submat
function.A runnable example
:ballot_box_with_check: Checklist
docs/src/
.[UNRELEASED]
section of the manually curatedCHANGELOG.md
file for this repository.