Merge branch 'main' into 505-dia-nn-params-modification-parsing-goes-…

…wrong-in-older-versions

proteobench/io/params/alphadia.py

@@ -237,11 +237,14 @@ def extract_params(fname: str) -> ProteoBenchParameters:
     Returns:
         ProteoBenchParameters: An object containing the extracted parameters.
     """
-    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])
+    try:
+        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])
+    except:
+        lines = [l for l in fname.read().decode("utf-8").splitlines() if "──" in l]
+        version = extract_file_version(lines[6])
 
     line_generator = iter(lines)
     first_line = next(line_generator)

proteobench/io/params/maxquant.py

@@ -139,7 +139,7 @@ def extract_params(fname, ms2frac="FTMS") -> ProteoBenchParameters:
     params.ident_fdr_psm = None
     params.ident_fdr_peptide = float(record.loc["peptideFdr"].squeeze())
     params.ident_fdr_protein = float(record.loc["proteinFdr"].squeeze())
-    params.enable_match_between_runs = record.loc["matchBetweenRuns"].squeeze() == "True"
+    params.enable_match_between_runs = record.loc["matchBetweenRuns"].squeeze().lower() == "true"
     _precursor_mass_tolerance = record.loc[
         pd.IndexSlice["parameterGroups", "parameterGroup", "mainSearchTol", :]
     ].squeeze()

test/params/mqpar1.5.3.30_MBR_sel.json

@@ -6,7 +6,7 @@
     "ident_fdr_psm": null,
     "ident_fdr_peptide": 0.01,
     "ident_fdr_protein": 0.01,
-    "enable_match_between_runs": false,
+    "enable_match_between_runs": true,
     "precursor_mass_tolerance": "[-4.5 ppm, 4.5 ppm]",
     "fragment_mass_tolerance": "[-20 ppm, 20 ppm]",
     "enzyme": "Trypsin/P",