Grantham's substitution matrix

[KaparaNewbie]

Add support for R. Grantham's substitution matrix from his 1974 paper

Types of changes

• [x] :sparkles: New feature (A non-breaking change which adds functionality).
• [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
• [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).

: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 the load_submat and parse_ncbi_submat functions. Existing calls to PAM and BLOSUM aren't changed as a result. For the new GRANTHAM1974 matrix, I chose default_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 and parse_ncbi_submat functions.

    1. While the existing PAM and BLOSUM matrices describe changes between amino acids from an evolutionary perspective, Grantham's matrix provides a more direct measurement. This measurement, supplemented by a cutoff, may help to discern between radical and conservative amino acid replacements.
    2. As Grantham only dealt with the basic 20 amino acids, I needed to support a different default_mismatch compared to default_mismatch == 0 as in the original return value SubstitutionMatrix(scores, default_match=0, default_mismatch=0) in the final line of the parse_ncbi_submat function.

  • A runnable example

    julia> using BioAlignments
    julia> sm = GRANTHAM1974

:ballot_box_with_check: Checklist

• [X] :art: The changes implemented is consistent with the julia style guide.
• [x] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
• [x] :blue_book: I have added or updated relevant user and developer manuals/documentation in docs/src/.
• [ ] :ok: There are unit tests that cover the code changes I have made.
• [ ] :ok: The unit tests cover my code changes AND they pass.
• [ ] :pencil: I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
• [x] :ok: All changes should be compatible with the latest stable version of Julia.
• [x] :thought_balloon: I have commented liberally for any complex pieces of internal code.

[KaparaNewbie]

@MillironX, could you kindly review this?

[KaparaNewbie]

Thank you, @MillironX, for your very kind response. I think I addressed all your points (hopefully there are enough tests).

[codecov[bot]]

Codecov Report

Base: 88.20% // Head: 88.28% // Increases project coverage by +0.08% :tada:

Coverage data is based on head (28dd1f1) compared to base (9a6a37d). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #88 +/- ## ========================================== + Coverage 88.20% 88.28% +0.08% ========================================== Files 16 16 Lines 1178 1178 ========================================== + Hits 1039 1040 +1 + Misses 139 138 -1 ``` | [Impacted Files](https://codecov.io/gh/BioJulia/BioAlignments.jl/pull/88?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | Coverage Δ | | |---|---|---| | [src/submat.jl](https://codecov.io/gh/BioJulia/BioAlignments.jl/pull/88/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL3N1Ym1hdC5qbA==) | `98.44% <100.00%> (+0.77%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia)

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[KaparaNewbie]

Sounds good, thanks. Sorry about the .gitignore thing. My git skill is (still) embarrassingly noobish.