Merge pull request #254 from MannLabs/add_alphadia_reader

Add alphadia reader

alphabase/constants/const_files/psm_reader.yaml

@@ -1,3 +1,26 @@
+alphadia:
+  reader_type: alphadia
+  rt_unit: minute
+  fixed_C57: False
+  column_mapping:
+    'raw_name': 'run'
+    'sequence': 'sequence'
+    'charge': 'charge'
+    'rt': 'rt_observed'
+    'rt_start': 'rt_start'
+    'rt_stop': 'rt_stop'
+    'ccs': 'ccs'
+    'mobility': 'mobility'
+    'proteins': 'proteins'
+    'uniprot_ids': 'uniprot_ids'
+    'genes': 'genes'
+#    'scan_num': '' ?
+    'score': 'score'
+    'fdr': 'fdr'
+    'mods': 'mods'
+    'intensity': 'intensity'
+  modification_mapping_type: 'maxquant' # TODO: None?
+
 alphapept:
   reader_type: alphapept
   rt_unit: minute

alphabase/psm_reader/__init__.py

@@ -14,8 +14,17 @@
     "MSFraggerPepXMLReader",
     "SageReaderTSV",
     "SageReaderParquet",
+    "AlphaDiaReaderTsv",
+    "AlphaDiaReaderParquet",
 ]
 
+from alphabase.psm_reader.alphadia_reader import (
+    AlphaDiaReaderParquet,
+    AlphaDiaReaderTsv,
+)
+from alphabase.psm_reader.alphadia_reader import (
+    register_readers as register_alphadia_readers,
+)
 from alphabase.psm_reader.alphapept_reader import (
     AlphaPeptReader,
 )
@@ -70,3 +79,4 @@
 register_mq_readers()
 register_pf_readers()
 register_sage_readers()
+register_alphadia_readers()

alphabase/psm_reader/alphadia_reader.py

@@ -0,0 +1,34 @@
+"""Reader for AlphaDia data."""
+
+from abc import ABC
+
+import pandas as pd
+
+from alphabase.psm_reader.psm_reader import PSMReaderBase, psm_reader_provider
+
+
+class AlphaDiaReader(PSMReaderBase, ABC):
+    """Reader for AlphaDia data."""
+
+    _reader_type = "alphadia"
+
+    def _translate_modifications(self) -> None:
+        """Nothing to translate for AlphaDIA."""
+
+
+class AlphaDiaReaderTsv(AlphaDiaReader):
+    """Reader for AlphaDia TSV files."""
+
+
+class AlphaDiaReaderParquet(AlphaDiaReader):
+    """Reader for AlphaDia parquet files."""
+
+    def _load_file(self, filename: str) -> pd.DataFrame:
+        """Read a parquet file."""
+        return pd.read_parquet(filename)
+
+
+def register_readers() -> None:
+    """Register AlphaDIA reader."""
+    psm_reader_provider.register_reader("alphadia", AlphaDiaReaderTsv)
+    psm_reader_provider.register_reader("alphadia_parquet", AlphaDiaReaderParquet)

alphabase/psm_reader/msfragger_reader.py

@@ -150,7 +150,7 @@ def _pre_process(self, df: pd.DataFrame) -> pd.DataFrame:
         """MsFragger-specific preprocessing of output data."""
         df.fillna("", inplace=True)
         if "ion_mobility" in df.columns:
-            df["ion_mobility"] = df.ion_mobility.astype(float)
+            df["ion_mobility"] = df["ion_mobility"].astype(float)
         df[PsmDfCols.RAW_NAME] = df["spectrum"].str.split(".").apply(lambda x: x[0])
         df["to_remove"] = 0  # TODO: revisit
         self.column_mapping[PsmDfCols.TO_REMOVE] = "to_remove"

alphabase/psm_reader/psm_reader.py

@@ -300,12 +300,13 @@ def _load_modifications(self, origin_df: pd.DataFrame) -> None:  # noqa: B027 em
 
     def _translate_modifications(self) -> None:
         """Translate modifications to AlphaBase format."""
-        self._psm_df[PsmDfCols.MODS], unknown_mods = zip(
+        mods, unknown_mods = zip(
             *self._psm_df[PsmDfCols.MODS].apply(
                 translate_modifications,
                 mod_dict=self._modification_mapper.rev_mod_mapping,
             )
         )
+        self._psm_df[PsmDfCols.MODS] = mods
 
         # accumulate unknown mods
         unknown_mod_set = set()