Merge pull request #381 from MannLabs/alpharaw-ms-data-base

alpharaw hdf reader

alphadia/data/alpharaw_wrapper.py

@@ -5,6 +5,7 @@
 import numba as nb
 import numpy as np
 import pandas as pd
+from alpharaw import ms_data_base as alpharaw_ms_data_base
 from alpharaw import mzml as alpharaw_mzml
 from alpharaw import sciex as alpharaw_sciex
 from alpharaw import thermo as alpharaw_thermo
@@ -327,6 +328,13 @@ def jitclass(self):
         )
 
 
+class AlphaRawBase(AlphaRaw, alpharaw_ms_data_base.MSData_Base):
+    def __init__(self, raw_file_path: str, process_count: int = 10, **kwargs):
+        super().__init__(process_count=process_count)
+        self.load_hdf(raw_file_path)
+        self.process_alpharaw(**kwargs)
+
+
 class MzML(AlphaRaw, alpharaw_mzml.MzMLReader):
     def __init__(self, raw_file_path: str, process_count: int = 10, **kwargs):
         super().__init__(process_count=process_count)

alphadia/workflow/managers/raw_file_manager.py

@@ -61,13 +61,20 @@ def get_dia_data_object(
             shutil.copyfile(dia_data_path, tmp_dia_data_path)
             dia_data_path = tmp_dia_data_path
 
-        if file_extension.lower() == ".d" or file_extension.lower() == ".hdf":
+        if file_extension.lower() == ".d":
             raw_data_type = "bruker"
             dia_data = bruker.TimsTOFTranspose(
                 dia_data_path,
                 mmap_detector_events=self._config["general"]["mmap_detector_events"],
             )
 
+        elif file_extension.lower() == ".hdf":
+            raw_data_type = "alpharaw"
+            dia_data = alpharaw_wrapper.AlphaRawBase(
+                dia_data_path,
+                process_count=self._config["general"]["thread_count"],
+            )
+
         elif file_extension.lower() == ".raw":
             raw_data_type = "thermo"