Add support for reading Sage PSM files; various minor fixes

[ArthurDeclercq]

Added

• Add reader for Sage PSM files.

Changed

• psm: The default values of PSM.provenance_data, PSM.metadata and PSM.rescoring_features are now dict() instead of None.
• io.mzid.MzidReader: Attempt to parse retention time or scan start time cvParams from both SpectrumIdentificationResult as SpectrumIdentificationItem levels. Note that according to the mzIdentML specification document (v1.1.1) neither cvParams are expected to be present at either level.
• io.mzid.MzidReader: Prefer spectrum title cvParam over spectrumID attribute for PSM.spectrum_id as these titles always match to the peak list files. In this case, spectrumID is saved in metadata["mzid_spectrum_id"]. Fall back to spectrumID if spectrum title is absent.
• io.mzid.MzidWriter: PSM.retention_time is now written as cvParam retention time instead of scan start time, and to the SpectrumIdentificationItem level instead of the SpectrumIdentificationResult level, as theoretically in psm_utils, multiple PSMs for the same spectrum can have different values for retention_time.
• io.mzid.MzidWriter: Write PSM score as cvParam search engine specific score instead of userParam score.
• io.percolator.PercolatorTabWriter: For PIN-style files: Use SpecId instead of PSMId and write PSMScore and ChargeN columns by default.

Fixed

• peptidoform: ProForma mass modifications are now correctly parsed within the rename_modifications function.
• io.maxquant.MSMSReader: Correctly parse empty Proteins column to None
• io.mzid.MzidReader: Set PSM.retention_time to None instead of float('nan') if missing from the PSM file.
• io.percolator.PercolatorTabReader: Correctly parse Percolator peptidoform notation if no leading or trailing amino acids are present (e.g. .ACDK. instead of K.ACDK.E).
• io.percolator.PercolatorTabWriter: ScanNr is now correctly written as an integer counting from the first PSM in the file.
• io.percolator.PercolatorTabWriter: If no protein information is present, write the peptidoform preceded by PEP_ to the Proteins column.

[codecov-commenter]

Codecov Report

Patch coverage: 37.68% and project coverage change: -0.05 ⚠️

Comparison is base (638d19b) 41.52% compared to head (4dacc86) 41.48%.

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Additional details and impacted files

@@            Coverage Diff             @@
##             main      #31      +/-   ##
==========================================
- Coverage   41.52%   41.48%   -0.05%     
==========================================
  Files          18       19       +1     
  Lines        1416     1468      +52     
==========================================
+ Hits          588      609      +21     
- Misses        828      859      +31     

Impacted Files	Coverage Δ
psm_utils/io/maxquant.py	84.61% <ø> (ø)
psm_utils/io/mzid.py	29.71% <0.00%> (-0.29%)	⬇️
psm_utils/io/percolator.py	28.82% <20.00%> (-0.35%)	⬇️
psm_utils/io/sage.py	41.02% <41.02%> (ø)
psm_utils/peptidoform.py	31.47% <60.00%> (+0.78%)	⬆️
psm_utils/io/__init__.py	37.03% <100.00%> (+0.78%)	⬆️
psm_utils/psm.py	85.71% <100.00%> (ø)

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[lazear]

I just opened a fork to do this, should've checked here first! Thanks for implementing this

[RalfG]

@lazear, great to hear that you wanted to add Sage support! Feel free to take a look at the implementation and give feedback where needed.
One thing I noticed was that the Sage documentation lists the spectrum_q column, while the actual output file seems to contain a spectrum_fdr column instead.

[lazear]

@lazear, great to hear that you wanted to add Sage support! Feel free to take a look at the implementation and give feedback where needed. One thing I noticed was that the Sage documentation lists the spectrum_q column, while the actual output file seems to contain a spectrum_fdr column instead.

Thanks for the catch - this is what I get for using ChatGPT to write docs :)