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wfondrie / mokapot

Fast and flexible semi-supervised learning for peptide detection in Python
https://mokapot.readthedocs.io
Apache License 2.0
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Updated PepXML parser for open modification search results #9

Closed wfondrie closed 3 years ago

wfondrie commented 3 years ago

The PepXML parser lacked the option to bin modification masses in the case of an open modification search. This is necessary when grouping peptides for peptide-level confidence estimation, so that peptides with the same modification, but with slight mass deviations, are considered together.

This PR adds the open_modification_bin_size parameter to the read_pepxml() function.

codecov-io commented 3 years ago

Codecov Report

Merging #9 (481a737) into master (d188408) will increase coverage by 5.83%. The diff coverage is 50.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master       #9      +/-   ##
==========================================
+ Coverage   70.44%   76.28%   +5.83%     
==========================================
  Files          15       15              
  Lines        1357     1362       +5     
==========================================
+ Hits          956     1039      +83     
+ Misses        401      323      -78
Impacted Files Coverage Δ
mokapot/parsers/pepxml.py 82.20% <50.00%> (+69.81%) :arrow_up:

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