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added protein n-gram#6

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jspaezp wants to merge 5 commits intomainfrom
feature/annotate_proteins
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added protein n-gram#6
jspaezp wants to merge 5 commits intomainfrom
feature/annotate_proteins

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@jspaezp jspaezp commented Dec 12, 2023

This adds a data structure that helps annotate peptide sequences to protein uniprot ids.
This is needed nowadays because the mokapot workflow drops the proteins column (since it is very expensive in memory).

It also adds a script to add protein annotations to a .blib/.elib. Before I make this a real PR I will add some data to test it programmatically (messing with it locally works).

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codecov bot commented Dec 12, 2023

Codecov Report

❌ Patch coverage is 53.77358% with 49 lines in your changes missing coverage. Please review.
✅ Project coverage is 46.34%. Comparing base (40dfebd) to head (b3faaa8).
⚠️ Report is 2 commits behind head on main.

Files with missing lines Patch % Lines
petasus/scripts/add_peptidetoprotein.py 0.00% 42 Missing ⚠️
petasus/protein_ngram.py 89.06% 7 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main       #6      +/-   ##
==========================================
+ Coverage   43.20%   46.34%   +3.14%     
==========================================
  Files           8       10       +2     
  Lines         250      356     +106     
==========================================
+ Hits          108      165      +57     
- Misses        142      191      +49     

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