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added protein n-gram #6

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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

Attention: 49 lines in your changes are missing coverage. Please review.

Comparison is base (40dfebd) 43.20% compared to head (b3faaa8) 46.34%.

Files 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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