changes from stream mzml reading to sequential

bigbio · Mar 8, 2025 · 68d9e89 · 68d9e89
1 parent 15ed5d7
commit 68d9e89
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/.markdownlint.json b/.markdownlint.json
@@ -0,0 +1,5 @@
+{
+  "MD033": {
+    "allowed_elements": ["details", "summary"]
+  }
+}
diff --git a/quantmsutils/mzml/mzml_statistics.py b/quantmsutils/mzml/mzml_statistics.py
@@ -227,6 +227,7 @@ def transform_mzml_spectrum(
         # Extract peaks data
         mz_array, intensity_array = spectrum.get_peaks()
         peak_count = len(mz_array)
+        scan_id = self._extract_scan_id(spectrum)
 
         # Basic spectrum properties
         ms_level = spectrum.getMSLevel()
@@ -252,7 +253,6 @@ def transform_mzml_spectrum(
 
             # Extract spectrum ID for ID-only mode
             if self.id_only:
-                scan_id = self._extract_scan_id(spectrum)
                 self.psm_parts.append(
                     {
                         SCAN: scan_id,
@@ -273,7 +273,7 @@ def transform_mzml_spectrum(
                 intensity = first_precursor_calculated["intensity"]
 
             row_data = {
-                SCAN: spectrum.getNativeID(),
+                SCAN: scan_id,
                 MS_LEVEL: ms_level,
                 NUM_PEAKS: peak_count,
                 BASE_PEAK_INTENSITY: base_peak_intensity,
@@ -297,7 +297,7 @@ def transform_mzml_spectrum(
         else:
             # Process MS1
             row_data = {
-                SCAN: spectrum.getNativeID(),
+                SCAN: scan_id,
                 MS_LEVEL: ms_level,
                 CHARGE: None,
                 NUM_PEAKS: peak_count,