Merge pull request #222 from MannLabs/sage-spec-idx

FIX Sage spec idx

alphabase/psm_reader/sage_reader.py

@@ -538,17 +538,31 @@ def _get_annotated_mod_df() -> pd.DataFrame:
     ]
 
 
-def _sage_spec_idx_from_scan_nr(scan_nr: str) -> int:
+def _sage_spec_idx_from_scan_nr(scan_indicator_str: str) -> int:
     """Extract the spectrum index from the scan_nr field in Sage output.
+    Sage uses 1-based indexing for spectra, so we need to subtract 1 to convert to 0-based indexing.
 
     Parameters
     ----------
 
-    scan_nr : str
-        The scan_nr field in Sage output.
+    scan_indicator_str : str
+        The scan_indicator_str field in Sage output.
+        e.g. `'controllerType=0 controllerNumber=1 scan=7846'`
+
+    Returns
+    -------
+
+    int
+        The 0-based spectrum index.
+
+    Examples
+    --------
+
+    >>> _sage_spec_idx_from_scan_nr('controllerType=0 controllerNumber=1 scan=7846')
+    7845
 
     """
-    return int(scan_nr.split("=")[-1])
+    return int(re.search(r"scan=(\d+)", scan_indicator_str).group(1)) - 1
 
 
 class SageReaderBase(PSMReaderBase):

nbs_tests/psm_reader/sage_reader.ipynb

@@ -47,7 +47,7 @@
    "outputs": [],
    "source": [
     "#| hide\n",
-    "assert _sage_spec_idx_from_scan_nr('controllerType=0 controllerNumber=1 scan=7846') == 7846"
+    "assert _sage_spec_idx_from_scan_nr('controllerType=0 controllerNumber=1 scan=7846') == 7845"
    ]
   },
   {
@@ -195,7 +195,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "python3",
+   "display_name": "alpha",
    "language": "python",
    "name": "python3"
   },