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Fasta2speclib refactoring #193

Merged
merged 15 commits into from
Feb 27, 2023
Merged

Fasta2speclib refactoring #193

merged 15 commits into from
Feb 27, 2023

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RalfG
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@RalfG RalfG commented Feb 21, 2023 •
edited

Added

  • fasta2speclib: Improved workflow for generating spectral libraries starting from a FASTA file, with new configuration options. ⚠️ These changes break compatibility with the previous configuration files. ⚠️
    • Support for C-terminal modifications
    • Differentiate between peptide and protein termini for variable modifications
    • Allow filtering of peptides based on precursor m/z
    • Allow semi-specific cleavage
    • Allow non-specific cleavage
    • Allow setting of a maximum of variable modifications per peptide
    • Add tests for modification assignment

Changed

  • Change logging of model configuration to debug level

Removed

  • fasta2speclib: Removed support for Elude-based RT predictions, RT predictions file, PEPREC filter, saving temporary PEPREC files

Fixed

  • Remove unsupported argument for mzml.read
  • spectrum_output: Fix CSV output to always use \n line terminators
  • spectrum_output: Use semi-colon for spectronaut CSV output
  • DeepLC integration: Disable PyGAM for default calibration on iRT peptides (led to poor calibration)

RalfG and others added 7 commits February 15, 2023 14:00
@RalfG
- Specify lineterminators in DataFrame.to_csv
3e4935d 
- Specify group_keys in DataFrame.groupby
- Change logging of model configuration to debug level
@RalfG
Completely refactor fasta2speclib; implement new features:
7630502 
- Support for C-terminal modifications
- Differentiate between peptide and protein termini for variable modifications
- Allow filtering of peptides based on precursor m/z
- Allow semi-specific cleavage
- Allow setting of a maximum of variable modifications per peptide
- Disable PyGAM for DeepLC calibration on iRT peptides (leads to strange predictions)
- Add tests for modification assignment
- Removed support for: Elude-based RT predictions, RT predictions file, PEPREC filter, saving temporary PEPREC files
@RalfG
Fix type hints
3830204
@RalfG
Use semi-colon for spectronaut CSV output
7623bb5
@RalfG
Remove unsupported argument for mzml.read; Add modstring info to exce…
4f2883a 
…ption raise
@RalfG
Restructure as class to allow control over individual workflow steps
e05d6b3
@ArthurDeclercq
add protein list to peprec
9777b20
@ArthurDeclercq ArthurDeclercq added this to the v3.10.2 milestone Feb 26, 2023
@RalfG RalfG linked an issue Feb 26, 2023 that may be closed by this pull request
fasta2speclib feature requests #188
Closed
@RalfG RalfG marked this pull request as ready for review February 26, 2023 23:23
@RalfG RalfG modified the milestones: v3.10.2, 3.11.0 Feb 26, 2023
@RalfG RalfG merged commit 2a104da into releases Feb 27, 2023
@RalfG RalfG deleted the fasta2speclib-refactoring branch February 27, 2023 00:33
@RalfG RalfG mentioned this pull request Feb 27, 2023
Closed
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fasta2speclib feature requests
2 participants
@RalfG @ArthurDeclercq