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v3.10.0

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@RalfG RalfG released this 01 Feb 12:38
· 254 commits to releases since this release
v3.10.0
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Learn about vigilant mode.

Added

  • Added support for mzML spectrum files (both for evaluating models and for extracting feature vectors).
  • New argument spectrum_id_pattern: Regular expression pattern to apply to spectrum titles before matching to peptide file entries.
  • When using MS²PIP as class instance, the resulting pred_and_emp dataframe can also be returned (instead of writing to a file) when setting return_results to True.
  • If requested, retention time prediction with DeepLC is now also enabled if spectrum file is given. This feature was previously only enabled if only a peptide file was given.

Changed

  • Improved logging: Use Rich library for logging, show time stamps and message log levels.
  • MS²PIP now shows a progress bar instead of a wall of text to display prediction progress.
  • fasta2speclib: Improved algorithm for variable modification assignment. Combinatorial explosion from variable modifications is now reduced by setting a maximum of modified residues per peptide, instead of arbitrarily selecting a maximum of potentially modified sites per peptide.
  • Update README.md (Switch from BadGen to Shields.io).
  • Switch to Pyteomics MGF reader.
  • Avoid SciPy dependency.
  • More optimal use of Numpy in calc_correlations.
  • Remove poetry.lock (not used, avoid unneeded Dependabot PRs).

Fixed

  • Vastly improved computational speed and reduced memory usage when using XGBoost model files for prediction in combination with providing a spectrum file (XGB prediction step is now moved out of multiprocessing).
  • For optimal performance, feature vectors for predictions from XGBoost model files now also uses the traditional ms2pipC.py multiprocessing system.
  • fasta2speclib: Fixed issue where modified versions of peptide were duplicated.
  • spectrum_output: Various fixes in MSP spectral library file writing for DIA-NN compatibility: Write m/z error of 0.0 for each predicted peak in peak annotation string, ensure modifications in MSP Mods field are sorted by position, use RetentionTime instead of RTINSECONDS in comments field.
  • Fixed double spectrum_utils entry in requirements.
  • Updated python_requires to minimal 3.7, following previously updated test grid.
  • Fix spectrum_utils modification off-by-one bug (had no consequences except for plot annotations).
  • Fix typo in write_amino_acid_masses function name.
  • Fix missing comma in the setup.py.

Removed

  • Removed unsupported Tableau output file option
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