io.mzid: Fix usage of score_key

compomics · Sep 19, 2023 · aea3bc0 · aea3bc0
1 parent 5f3939d
commit aea3bc0
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/psm_utils/io/mzid.py b/psm_utils/io/mzid.py
@@ -133,7 +133,7 @@ def __init__(self, filename: str | Path, *args, score_key: str = None, **kwargs)
         """
         super().__init__(filename, *args, **kwargs)
         self._non_metadata_keys = ["ContactRole", "passThreshold"]
-        self._score_key = None
+        self._score_key = score_key
         self._rt_key = None
         self._spectrum_rt_key = None
         self._qvalue_key = None
@@ -260,16 +260,15 @@ def _get_peptide_spectrum_match(
             psm_spectrum_id = spectrum_id
 
         try:
-            score = sii[self.score_key]
+            score = sii[self._score_key]
         except KeyError:
             score = None
-
         psm = PSM(
             peptidoform=peptidoform,
             spectrum_id=psm_spectrum_id,
             run=run,
             is_decoy=is_decoy,
-            score=sii[self._score_key] if self._score_key else None,
+            score=score,
             qvalue=sii[self._qvalue_key] if self._qvalue_key else None,
             pep=sii[self._pep_key] if self._pep_key else None,
             precursor_mz=precursor_mz,
@@ -295,7 +294,8 @@ def _get_non_metadata_keys(self, keys: list):
             "Modification",
         ]
         # Get the score key and add to default keys
-        self._score_key = self._infer_score_name(keys)
+        if not self._score_key:
+            self._score_key = self._infer_score_name(keys)
         if self._score_key:
             default_keys.append(self._score_key)
         else: