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Generalize whitespace handling in splitting modification column FragPipe#146

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RalfG merged 1 commit into
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fix-fragpipe-mod-splitting
May 12, 2026
Merged

Generalize whitespace handling in splitting modification column FragPipe#146
RalfG merged 1 commit into
mainfrom
fix-fragpipe-mod-splitting

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@rodvrees
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@rodvrees rodvrees commented May 12, 2026

Small improvement to the parsing logic for modifications in the _parse_peptidoform function in psm_utils/io/fragpipe.py. I am not sure of the reason why, but sometimes FragPipe output separates modification by ", " and sometimes just ",". Could have to do with versioning. This change ensures that any extra whitespace around modification entries is removed, making the parsing more robust to formatting inconsistencies.

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codecov Bot commented May 12, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 71.97%. Comparing base (22e6442) to head (79fe780).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #146   +/-   ##
=======================================
  Coverage   71.97%   71.97%           
=======================================
  Files          32       32           
  Lines        3247     3247           
=======================================
  Hits         2337     2337           
  Misses        910      910           
Flag Coverage Δ
unittests 71.97% <100.00%> (ø)

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@rodvrees rodvrees requested review from RalfG and paretje May 12, 2026 15:27
@RalfG RalfG merged commit af24473 into main May 12, 2026
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@RalfG RalfG deleted the fix-fragpipe-mod-splitting branch May 12, 2026 18:05
@RalfG RalfG added the bug Something isn't working label May 13, 2026
@RalfG RalfG added this to the v1.5.3 milestone May 13, 2026
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