changes for mumble implementation

compomics · Nov 21, 2024 · 295e37f · 295e37f
1 parent c51cd34
commit 295e37f
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Showing 3 changed files with 2 additions and 45 deletions.
diff --git a/ms2rescore/feature_generators/ms2.py b/ms2rescore/feature_generators/ms2.py
@@ -23,7 +23,6 @@
 
 FRAGMENTATION_MODELS = {
     "cidhcd": FragmentationModel.CidHcd,
-    "etcid": FragmentationModel.Etcid,
     "etd": FragmentationModel.Etd,
     "ethcd": FragmentationModel.Ethcd,
     "all": FragmentationModel.All,
@@ -148,28 +147,6 @@ def _calculate_features(self, psm_list: PSMList, spectrum_file: str) -> List:
 
             else:
                 psm.rescoring_features.update({"hyperscore": np.nan})
-        # with multiprocessing.Pool(self.processes) as pool:
-        #     counts_failed = 0
-        #     for psm, features in zip(
-        #         psm_list,
-        #         track(
-        #             pool.imap(
-        #                 self._calculate_spectrum_features_wrapper,
-        #                 zip(psm_list, annotated_spectra),
-        #                 chunksize=1000,
-        #             ),
-        #             total=len(psm_list),
-        #             description="Calculating MS2 features...",
-        #             transient=True,
-        #         ),
-        #     ):
-        #         if features:
-        #             psm.rescoring_features.update(features)
-
-        #         else:
-        #             counts_failed += 1
-        # if counts_failed > 0:
-        #     logger.warning(f"Failed to calculate features for {counts_failed} PSMs")
 
     @staticmethod
     def _read_spectrum_file(spectrum_filepath: str) -> Union[mzml.PreIndexedMzML, mgf.IndexedMGF]:
@@ -246,10 +223,6 @@ def _calculate_spectrum_features(self, psm, annotated_spectrum):
             / (len(b_ions_matched) + len(y_ions_matched)),
         }
 
-    def _calculate_spectrum_features_wrapper(self, psm_spectrum_tuple):
-        psm, spectrum = psm_spectrum_tuple
-        return self._calculate_spectrum_features(psm, spectrum)
-
     def _annotate_spectrum(self, psm, pyteomics_spectrum):
 
         spectrum = RawSpectrum(
@@ -272,17 +245,6 @@ def _annotate_spectrum(self, psm, pyteomics_spectrum):
 
         return annotated_spectrum.spectrum
 
-    def _calculate_hyperscore(self, psm, spectrum):
-        pass
-
-    def _calculate_fragmentation_features(self, psm, annotated_spectrum):
-        pass
-
-
-# TODO: keep this here?
-def modification_evidence():
-    return
-
 
 def _annotated_spectrum_to_mzint(annotated_spectrum, ion_types=["b", "y"]):
 

diff --git a/ms2rescore/parse_psms.py b/ms2rescore/parse_psms.py
@@ -104,13 +104,9 @@ def parse_psms(config: Dict, psm_list: Union[PSMList, None]) -> PSMList:
                 psm.rescoring_features = {}
 
         psm_handler = PSMHandler(
-            **mumble_config,  # TODO how do we store config for mumble?
+            **mumble_config,
         )
-        psm_list = psm_handler.add_modified_psms(
-            psm_list, generate_modified_decoys=True, keep_original=True
-        )
-        if mumble_config["output_file"]:
-            psm_handler.write_modified_psm_list(psm_list, mumble_config["output_file"])
+        psm_list = psm_handler.add_modified_psms(psm_list)
 
     return psm_list
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -50,7 +50,6 @@ dependencies = [
     "pyteomics>=4.7.2",
     "rich>=12",
     "tomli>=2; python_version < '3.11'",
-    "mumble"
 ]
 
 [project.optional-dependencies]