ms2rescore 3.1.0.dev3__tar.gz → 3.1.0.dev4__tar.gz

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  1. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/PKG-INFO +1 -1
  2. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/__init__.py +1 -1
  3. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/rescoring_engines/mokapot.py +10 -8
  4. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/LICENSE +0 -0
  5. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/README.md +0 -0
  6. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/__main__.py +0 -0
  7. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/config_parser.py +0 -0
  8. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/core.py +0 -0
  9. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/exceptions.py +0 -0
  10. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/__init__.py +0 -0
  11. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/base.py +0 -0
  12. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/basic.py +0 -0
  13. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/deeplc.py +0 -0
  14. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/im2deep.py +0 -0
  15. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/ionmob.py +0 -0
  16. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/maxquant.py +0 -0
  17. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/feature_generators/ms2pip.py +0 -0
  18. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/gui/__init__.py +0 -0
  19. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/gui/__main__.py +0 -0
  20. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/gui/app.py +0 -0
  21. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/gui/function2ctk.py +0 -0
  22. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/gui/widgets.py +0 -0
  23. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/__init__.py +0 -0
  24. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/config_default.json +0 -0
  25. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/config_default_tims.json +0 -0
  26. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/config_schema.json +0 -0
  27. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/img/__init__.py +0 -0
  28. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/img/config_icon.png +0 -0
  29. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/img/github-mark-white.png +0 -0
  30. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/img/github-mark.png +0 -0
  31. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/img/ms2rescore_logo.png +0 -0
  32. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/img/program_icon.ico +0 -0
  33. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/package_data/ms2rescore-gui-theme.json +0 -0
  34. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/parse_psms.py +0 -0
  35. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/parse_spectra.py +0 -0
  36. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/__init__.py +0 -0
  37. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/__main__.py +0 -0
  38. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/charts.py +0 -0
  39. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/generate.py +0 -0
  40. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/__init__.py +0 -0
  41. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/about.html +0 -0
  42. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/base.html +0 -0
  43. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/config.html +0 -0
  44. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/features.html +0 -0
  45. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/log.html +0 -0
  46. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/metadata.html +0 -0
  47. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/overview.html +0 -0
  48. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/stats-card.html +0 -0
  49. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/style.html +0 -0
  50. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/target-decoy.html +0 -0
  51. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/templates/texts.toml +0 -0
  52. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/report/utils.py +0 -0
  53. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/rescoring_engines/__init__.py +0 -0
  54. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/rescoring_engines/percolator.py +0 -0
  55. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/utils.py +0 -0
  56. {ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/pyproject.toml +0 -0
{ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: ms2rescore
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- Version: 3.1.0.dev3
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+ Version: 3.1.0.dev4
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  Summary: MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.
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  Keywords: MS2Rescore,MS2PIP,DeepLC,Percolator,proteomics,mass spectrometry,peptide identification,rescoring,machine learning
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  Author: Ana Sílvia C. Silva, Robbin Bouwmeester, Louise Buur
{ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/__init__.py RENAMED
@@ -1,6 +1,6 @@
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  """MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs."""
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- __version__ = "3.1.0-dev3"
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+ __version__ = "3.1.0-dev4"
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  from warnings import filterwarnings
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{ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/ms2rescore/rescoring_engines/mokapot.py RENAMED
@@ -111,17 +111,19 @@ def rescore(
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  psm_list["pep"] = q[:, 2]
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  # Repeat for peptide-level scores
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- peptide_info = pd.concat(
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- [
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- confidence_results.confidence_estimates["peptides"].set_index(["peptide"])[keys],
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- confidence_results.decoy_confidence_estimates["peptides"].set_index(["peptide"])[keys],
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- ],
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- axis=0,
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- ).to_dict(orient="index")
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+ peptides_targets = confidence_results.confidence_estimates["peptides"].set_index(
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+ ["peptide", "run"]
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+ )[keys]
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+ peptides_decoys = confidence_results.decoy_confidence_estimates["peptides"].set_index(
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+ ["peptide", "run"]
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+ )[keys]
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+ peptide_info = pd.concat([peptides_targets, peptides_decoys], axis=0).to_dict(orient="index")
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  peptidoform_without_charge = re.compile(r"(/\d+$)")
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  for psm in psm_list:
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- peptide_scores = peptide_info[peptidoform_without_charge.sub("", str(psm.peptidoform), 1)]
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+ peptide_scores = peptide_info[
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+ (peptidoform_without_charge.sub("", str(psm.peptidoform), 1), psm.run)
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+ ]
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  psm.metadata.update(
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  {
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  "peptide_score": peptide_scores["mokapot score"],
{ms2rescore-3.1.0.dev3 → ms2rescore-3.1.0.dev4}/LICENSE RENAMED
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