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Add more conveniences for noncoding nucleotide alphabets #81

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Add more conveniences for noncoding nucleotide alphabets #81

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@olgabot olgabot commented Jul 16, 2020

Many thanks to contributing to czbiohub/sencha!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • Ensure the test suite passes with pytest . (command to run: pytest or make coverage if you want to see which lines don't have tests yet)
  • Make sure your code is linted and autoformatted using black (black . --check).
  • Documentation in usage.md is updated
  • README.md is updated

olgabot and others added 30 commits May 28, 2020 14:12
@olgabot
Add residues to ignore, make sure seuqence is longer than k-mer size
506acea
@olgabot
Add test to error out if there are too many bloom filter collisions
811c9c4
@olgabot
Add khmer's expected collisions calculator to check for bloom filter …
3489159 
…size
@olgabot
Use index-specific version of alphabets and k-mer sizes that doesn't …
5b7f7bc 
…allow for failures
@olgabot
Rename make_peptide_bloom_filter --> make_peptide_index
61ffc6c
@olgabot
Add test for if there are too many observed k-mers relative to theore…
d0516ae 
…tical k-mers
@olgabot
Update index tests to only test for "good" k-mer sizes and molecule e…
e0f9ee2 
…ncoding combinations
@olgabot
Rename internal variables: peptide_bloom_filter --> peptide_index
e89cbdd
@olgabot
Black formatting
ce95b10
@olgabot
more bloom_filter --> index renaming
4fd03df
@olgabot
Move BEST_KSIZES to constants_index.py, update ksizes
582fd75
@olgabot
Add docstring to score_single_translation
c07f8fa
@olgabot
Add .fa to peptide_bloom_filter path
269a23e
@olgabot
Manually set max_observed_fraction, fixes for checking raise ValueError
d53b2cb
@olgabot
Make sure test_score_single_translation scores only one translation
741cabf
@olgabot
Add updated bloomfilter/indexes for testing
240b03a
@olgabot
Black formatting
57c8682
@olgabot
Refactor checks of protein indices into their own methods
e08fda2
@olgabot
Add bloom filter/index files for testing
57681cd
@olgabot
Add docstrings
3f421c7
@olgabot
Update HISTORY.md
8e4880a
@olgabot
Add note about ksize and tablesize to README
f7f517c
@olgabot
Rename HISTORY.md --> CHANGELOG.md
71a7509
@olgabot
Update test files for csv
8bf12a3
@olgabot
Assert for the correct class
15c8092
@olgabot
Update make_peptide_index test
1bd8609
@olgabot
Black formatting
d9551fb
@olgabot
Add --force option for creating peptide index with too small of table…
5c964e2 
…s or ksize too small
@olgabot
Add more docstrings
b2cf40c
@olgabot @pranathivemuri
Update CHANGELOG.md
c751010 
Co-authored-by: Pranathi Vemuri <[email protected]>
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