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Filter reversed #49

Merged
merged 6 commits into from
Oct 11, 2023
Merged

Filter reversed #49

merged 6 commits into from
Oct 11, 2023

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enryH
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@enryH enryH commented Sep 27, 2023

  • filter peptides from reversed protein sequences.

Henry added 2 commits September 27, 2023 15:09
🐛 remove peptides from reversed protein groups
1da36a6 
- reversed decoy sequence matches should be removed (it's only a few)
🐛 set index correctly
9725406
@enryH enryH changed the base branch from main to dev September 27, 2023 15:37
Henry added 4 commits September 29, 2023 15:55
🐛 remove reversed sequences from evidence
6d8ecbf 
- precursors from reversed protein sequences are removed from the evidence
  table
- adapt code to use local information (yaml files)
🐛 make pandas 2.0 compatible
12218c5 
- append is depreciated.
🎨🐛 reverse column for evidence, rename all dumps
0fcc086 
- rename also protein groups and precursors (evidence) dumps
- drop entries from reversed sequences in evidence files
🎨✨ unify and showcase internals, add IDs
8b3ffc8 
- function loading and filtering data
- add IDs making it possible to make precursors (Evidence IDs),
  Peptide ID and Protein Groups IDs to each other.
  in a file the id column is always "id" (e.g. proteinGroups.txt id column = Protein Groups IDs in the other two)
@enryH enryH marked this pull request as ready for review October 11, 2023 12:28
@enryH enryH merged commit cfc5fe5 into dev Oct 11, 2023
6 checks passed
@enryH enryH deleted the filter_reversed branch October 11, 2023 13:01
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