Allow missing precursor charge in mzML

compomics · Sep 18, 2023 · 42003cf · 42003cf
1 parent d220a04
commit 42003cf
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/ms2pip/__init__.py b/ms2pip/__init__.py
@@ -10,7 +10,7 @@
 )
 
 
-from ms2pip.core import (
+from ms2pip.core import (  # noqa: F401 E402
     predict_single,
     predict_batch,
     predict_library,

diff --git a/ms2pip/spectrum_input.py b/ms2pip/spectrum_input.py
@@ -69,12 +69,16 @@ def read_mzml(spectrum_file: str) -> Generator[ObservedSpectrum, None, None]:
                 precursor = spectrum["precursorList"]["precursor"][0]["selectedIonList"][
                     "selectedIon"
                 ][0]
+                try:
+                    precursor_charge = precursor["charge state"]
+                except KeyError:
+                    precursor_charge = None
                 spectrum = ObservedSpectrum(
                     identifier=spectrum["id"],
                     mz=spectrum["m/z array"],
                     intensity=spectrum["intensity array"],
                     precursor_mz=precursor["selected ion m/z"],
-                    precursor_charge=precursor["charge state"],
+                    precursor_charge=precursor_charge,
                 )
                 yield spectrum