Merge pull request #562 from Proteobench/fix-general-dia-issues

Fix several param parsing issues from #560

proteobench/io/params/alphadia.py

@@ -191,23 +191,6 @@ def extract_file_version(line: str) -> str:
     return match.group(1) if match else None
 
 
-def add_fdr_parameters(parameter_dict: dict, parsed_settings: dict) -> None:
-    """
-    Adds FDR parameters (e.g., ident_fdr_psm, ident_fdr_peptide) to the parameter dictionary.
-
-    Args:
-        parameter_dict (dict): The dictionary where the FDR parameters will be added.
-        parsed_settings (dict): The parsed settings containing the FDR values.
-    """
-    fdr_value = float(parsed_settings["fdr"]["fdr"])
-    fdr_level = parsed_settings["fdr"]["group_level"].strip()
-
-    level_mapping = {"proteins": "ident_fdr_protein"}
-    fdr_parameters = {"ident_fdr_psm": None, "ident_fdr_peptide": None, "ident_fdr_protein": None}
-    fdr_parameters[level_mapping[fdr_level]] = fdr_value
-    parameter_dict.update(fdr_parameters)
-
-
 def get_min_max(list_of_elements: list) -> Tuple[int, int]:
     """
     Extracts the minimum and maximum values from a list of elements.
@@ -241,10 +224,13 @@ def extract_params(fname: str) -> ProteoBenchParameters:
         with open(fname) as f:
             lines_read = f.readlines()
             lines = [line for line in lines_read if "──" in line]
-        version = extract_file_version(lines_read[6])
+            version_line = [line for line in lines_read if "version" in line][0]
+        version = extract_file_version(version_line)
     except:
-        lines = [l for l in fname.read().decode("utf-8").splitlines() if "──" in l]
-        version = extract_file_version(lines[6])
+        lines_read = [l for l in fname.read().decode("utf-8").splitlines()]
+        lines = [line for line in lines_read if "──" in line]
+        version_line = [line for line in lines_read if "version" in line][0]
+        version = extract_file_version(version_line)
 
     line_generator = iter(lines)
     first_line = next(line_generator)
@@ -255,17 +241,22 @@ def extract_params(fname: str) -> ProteoBenchParameters:
     precursor_charges = get_min_max(parsed_settings["library_prediction"]["precursor_charge"])
 
     prec_tol = float(parsed_settings["search"]["target_ms1_tolerance"])
+    prec_tol_string = f"[-{prec_tol} ppm, {prec_tol} ppm]"
     frag_tol = float(parsed_settings["search"]["target_ms2_tolerance"])
+    frag_tol_string = f"[-{frag_tol} ppm, {frag_tol} ppm]"
 
     parameters = {
         "software_name": "AlphaDIA",
         "search_engine": "AlphaDIA",
         "software_version": version,
         "search_engine_version": version,
         "enable_match_between_runs": False,
-        "precursor_mass_tolerance": prec_tol,
-        "fragment_mass_tolerance": frag_tol,
-        "enzyme": parsed_settings["library_prediction"]["enzyme"].strip(),
+        "precursor_mass_tolerance": prec_tol_string,
+        "fragment_mass_tolerance": frag_tol_string,
+        "ident_fdr_psm": parsed_settings["fdr"]["fdr"],
+        "ident_fdr_peptide": None,
+        "ident_fdr_protein": parsed_settings["fdr"]["fdr"],
+        "enzyme": parsed_settings["library_prediction"]["enzyme"].strip().capitalize(),
         "allowed_miscleavages": int(parsed_settings["library_prediction"]["missed_cleavages"]),
         "min_peptide_length": peptide_lengths[0],
         "max_peptide_length": peptide_lengths[1],
@@ -280,7 +271,6 @@ def extract_params(fname: str) -> ProteoBenchParameters:
         "predictors_library": "Built-in",
     }
 
-    add_fdr_parameters(parameters, parsed_settings)
     return ProteoBenchParameters(**parameters)
 
 

proteobench/io/params/diann.py

@@ -217,6 +217,10 @@ def parse_protein_inference_method(cmdline_dict: dict) -> str:
             return pg_level_mapping[pg_setting]
         except KeyError:
             Exception(f"Unexpected setting passed to --pg-level in diann.exe: {pg_setting}")
+    else:
+        return (
+            "Genes"  # Default value, when --pg-level is not changed in the GUI it does not appear in the command string
+        )
 
 
 def parse_quantification_strategy(cmdline_dict: dict):

proteobench/io/params/fragger.py

@@ -160,7 +160,7 @@ def extract_params(file: BytesIO) -> ProteoBenchParameters:
 
     elif fragpipe_params.loc["diann.run-dia-nn"] == "true":
         params.ident_fdr_protein = fragpipe_params.loc["diann.q-value"]
-        params.ident_fdr_peptide = fragpipe_params.loc["diann.q-value"]
+        params.ident_fdr_peptide = None
         params.ident_fdr_psm = fragpipe_params.loc["diann.q-value"]
         params.abundance_normalization_ions = None
 

proteobench/io/params/spectronaut.py

@@ -35,7 +35,7 @@ def extract_value(lines: List[str], search_term: str) -> Optional[str]:
     return next((clean_text(line.split(search_term)[1]) for line in lines if search_term in line), None)
 
 
-def extract_mass_tolerance(lines: List[str], search_term: str) -> Optional[str]:
+def extract_mass_tolerance(lines: List[str], search_term: str, mass_analyzer="Orbitrap") -> Optional[str]:
     """
     Extract the mass tolerance value associated with a search term, with special handling for "System Default".
 
@@ -47,7 +47,13 @@ def extract_mass_tolerance(lines: List[str], search_term: str) -> Optional[str]:
         Optional[str]: The extracted mass tolerance value, or None if the search term is not found.
     """
     value = next((clean_text(line.split(search_term)[1]) for line in lines if search_term in line), None)
-    value = "40 ppm" if value == "System Default" else value
+    if value == "System Default":
+        if mass_analyzer in (["Orbitrap", "TOF", "BrukerTOF"]):
+            value = "40 ppm"
+        elif mass_analyzer == "WatersTOF":
+            value = "80 ppm"
+        elif mass_analyzer == "IonTrap":
+            value = "0.5 th"
     return value
 
 
@@ -102,7 +108,7 @@ def read_spectronaut_settings(file_path: str) -> ProteoBenchParameters:
     params.ident_fdr_psm = float(extract_value(lines, "Precursor Qvalue Cutoff:"))
     params.ident_fdr_peptide = None
     params.ident_fdr_protein = float(extract_value(lines, "Protein Qvalue Cutoff (Experiment):"))
-    params.enable_match_between_runs = None
+    params.enable_match_between_runs = False
     _precursor_mass_tolerance = extract_mass_tolerance(lines, "MS1 Mass Tolerance Strategy:")
     params.precursor_mass_tolerance = f"[-{_precursor_mass_tolerance}, {_precursor_mass_tolerance}]"
     _fragment_mass_tolerance = extract_mass_tolerance(lines, "MS2 Mass Tolerance Strategy:")

test/params/DIANN_1.7.16.log.csv

@@ -3,7 +3,7 @@ software_name,DIA-NN
 software_version,1.7.16
 search_engine,DIA-NN
 search_engine_version,1.7.16
-ident_fdr_psm,
+ident_fdr_psm,None
 ident_fdr_peptide,0.01
 ident_fdr_protein,0.01
 enable_match_between_runs,True
@@ -16,11 +16,8 @@ max_peptide_length,30
 fixed_mods,Carbamidomethyl (C)
 variable_mods,Oxidation (M)
 max_mods,1
-min_precursor_charge,
-max_precursor_charge,
-scan_window,10
+min_precursor_charge,None
+max_precursor_charge,None
 quantification_method,QuantUMS high-precision
-second_pass,False
-protein_inference,
-predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
+protein_inference,Genes
 abundance_normalization_ions,

test/params/DIANN_WU304578_report.log.csv

@@ -3,7 +3,7 @@ software_name,DIA-NN
 software_version,1.8.2 beta 8
 search_engine,DIA-NN
 search_engine_version,1.8.2 beta 8
-ident_fdr_psm,
+ident_fdr_psm,None
 ident_fdr_peptide,0.01
 ident_fdr_protein,0.01
 enable_match_between_runs,True
@@ -18,9 +18,6 @@ variable_mods,UniMod:35/15.994915/M
 max_mods,1
 min_precursor_charge,2
 max_precursor_charge,3
-scan_window,13
 quantification_method,QuantUMS high-precision
-second_pass,False
-protein_inference,
-predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
+protein_inference,Genes
 abundance_normalization_ions,

test/params/DIANN_output_20240229_report.log.csv

@@ -3,7 +3,7 @@ software_name,DIA-NN
 software_version,1.8.2 beta 22
 search_engine,DIA-NN
 search_engine_version,1.8.2 beta 22
-ident_fdr_psm,
+ident_fdr_psm,None
 ident_fdr_peptide,0.01
 ident_fdr_protein,0.01
 enable_match_between_runs,True
@@ -18,9 +18,6 @@ variable_mods,UniMod:35/15.994915/M
 max_mods,1
 min_precursor_charge,1
 max_precursor_charge,4
-scan_window,13
 quantification_method,QuantUMS high-accuracy
-second_pass,True
 protein_inference,Protein_names
-predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
 abundance_normalization_ions,

test/params/Version1_9_Predicted_Library_report.log.csv

@@ -3,7 +3,7 @@ software_name,DIA-NN
 software_version,1.9
 search_engine,DIA-NN
 search_engine_version,1.9
-ident_fdr_psm,
+ident_fdr_psm,None
 ident_fdr_peptide,0.01
 ident_fdr_protein,0.01
 enable_match_between_runs,True
@@ -18,9 +18,6 @@ variable_mods,"UniMod:35/15.994915/M,UniMod:1/42.010565/*n"
 max_mods,1
 min_precursor_charge,1
 max_precursor_charge,4
-scan_window,13
 quantification_method,QuantUMS high-precision
-second_pass,True
 protein_inference,Protein_names
-predictors_library,"{'RT': 'DIANN', 'IM': 'DIANN', 'MS2_int': 'DIANN'}"
 abundance_normalization_ions,

test/params/spectronaut_Experiment1_ExperimentSetupOverview_BGS_Factory_Settings.csv

@@ -6,7 +6,7 @@ search_engine_version,19.2.240905.62635
 ident_fdr_psm,0.01
 ident_fdr_peptide,
 ident_fdr_protein,0.01
-enable_match_between_runs,
+enable_match_between_runs,False
 precursor_mass_tolerance,"[-40 ppm, 40 ppm]"
 fragment_mass_tolerance,"[-40 ppm, 40 ppm]"
 enzyme,Trypsin/P
@@ -18,9 +18,9 @@ variable_mods,"Acetyl (Protein N-term), Oxidation (M)"
 max_mods,5
 min_precursor_charge,
 max_precursor_charge,
-scan_window,Dynamic
 quantification_method,MS2
-second_pass,directDIA+ (Deep)
 protein_inference,IDPicker
-predictors_library,False
 abundance_normalization_ions,True
+scan_window,Dynamic
+second_pass,directDIA+ (Deep)
+predictors_library,False

test_proline.csv

@@ -0,0 +1,23 @@
+,0
+software_name,ProlineStudio
+software_version,2.3.0-SNAPSHOT_2024-09-11T06:45:20Z_jenkins
+search_engine,Mascot
+search_engine_version,2.8.3
+ident_fdr_psm,0.01
+ident_fdr_peptide,
+ident_fdr_protein,
+enable_match_between_runs,True
+precursor_mass_tolerance,"[-10.0 ppm, 10.0 ppm]"
+fragment_mass_tolerance,"[-0.02 Da, 0.02 Da]"
+enzyme,Trypsin/P
+allowed_miscleavages,2
+min_peptide_length,7
+max_peptide_length,
+fixed_mods,Carbamidomethyl (C)
+variable_mods,Acetyl (Protein N-term); Oxidation (M)
+max_mods,
+min_precursor_charge,2
+max_precursor_charge,3
+quantification_method,
+protein_inference,
+abundance_normalization_ions,