minor changes to logging and other bugfixes

Author: ArthurDeclercq

ms2rescore/core.py

@@ -37,7 +37,9 @@ def rescore(configuration: Dict, psm_list: Optional[PSMList] = None) -> None:
         f"Running MS²Rescore with following configuration: {json.dumps(configuration, indent=4)}"
     )
     config = configuration["ms2rescore"]
-    output_file_root = config["output_path"]
+    output_file_root = config["output_path"].split(".intermidiate.")[
+        0
+    ]  # if no intermediate, takes full name
 
     # Write full configuration including defaults to file
     with open(output_file_root + ".full-config.json", "w") as f:

ms2rescore/parse_psms.py

@@ -84,7 +84,9 @@ def parse_psms(config: Dict, psm_list: Union[PSMList, None]) -> PSMList:
             {
                 "before_rescoring_score": psm.score,
                 "before_rescoring_qvalue": psm.qvalue,
-                "before_rescoring_pep": psm.pep if psm.pep is not None else float("nan"),
+                "before_rescoring_pep": psm.pep
+                if psm.pep is not None
+                else float("nan"),  # until fixed in psm_utils
                 "before_rescoring_rank": psm.rank,
             }
         )

ms2rescore/parse_spectra.py

@@ -84,8 +84,6 @@ def add_precursor_values(
     if np.any(np.isnan(mz_values)) or np.all(mz_values == 0):
         missing_data_types.add(MSDataType.precursor_mz)
 
-    LOGGER.debug("Missing data types: %s", missing_data_types)
-
     # Find data types that are both missing and required
     data_types_to_parse = missing_data_types & required_data_types
 
@@ -103,6 +101,11 @@ def add_precursor_values(
             "Spectrum path must be provided to parse precursor values that are not present in the"
             " PSM list."
         )
+    else:
+        LOGGER.debug(
+            "Missing required data types: %s. Parsing from spectrum files.",
+            ", ".join(str(dt) for dt in data_types_to_parse),
+        )
 
     # Get precursor values from spectrum files
     LOGGER.info("Parsing precursor info from spectrum files...")