#296: make saving of libraries optional

alphadia/constants/default.yaml

@@ -185,6 +185,9 @@ search_output:
   normalize_lfq: True
   # can be either "parquet" or "tsv"
   file_format: "tsv"
+  # whether to save the (MBR) library to the output directory
+  save_library: True
+  save_mbr_library: True
 
 # configuration for the optimization manager
 # initial parameters, will nbe optimized

alphadia/outputtransform.py

@@ -365,7 +365,11 @@ def build(
         )
         _ = self.build_stat_df(folder_list, psm_df=psm_df, save=True)
         _ = self.build_lfq_tables(folder_list, psm_df=psm_df, save=True)
-        _ = self.build_library(base_spec_lib, psm_df=psm_df, save=True)
+        _ = self.build_library(
+            base_spec_lib,
+            psm_df=psm_df,
+            save=self.config["general"]["save_mbr_library"],
+        )
 
         if self.config["transfer_library"]["enabled"]:
             _ = self.build_transfer_library(folder_list, save=True)
@@ -804,14 +808,10 @@ def build_library(
         precursor_number = len(mbr_spec_lib.precursor_df)
         protein_number = mbr_spec_lib.precursor_df.proteins.nunique()
 
-        # use comma to separate thousands
         logger.info(
             f"MBR spectral library contains {precursor_number:,} precursors, {protein_number:,} proteins"
         )
 
-        logger.info("Writing MBR spectral library to disk")
-        mbr_spec_lib.save_hdf(os.path.join(self.output_folder, "speclib.mbr.hdf"))
-
         if save:
             logger.info("Writing MBR spectral library to disk")
             mbr_spec_lib.save_hdf(os.path.join(self.output_folder, "speclib.mbr.hdf"))

alphadia/planning.py

@@ -361,11 +361,13 @@ def run(
         except Exception as e:
             _log_exception_event(e)
             raise e
+        finally:
+            self.clean()
 
         logger.progress("=================== Search Finished ===================")
 
     def clean(self):
-        if not self.config["library_loading"]["save_hdf"]:
+        if not self.config["general"]["save_library"]:
             os.remove(os.path.join(self.output_folder, "speclib.hdf"))