migration fix : truncate seq and save data with labels

Author: aditya0by0

chebai/preprocessing/migration/deep_go/migrate_deep_go_2_data.py

@@ -20,24 +20,28 @@ class DeepGo2DataMigration:
         (https://doi.org/10.1093/bioinformatics/btx624)
     """
 
-    # https://github.com/bio-ontology-research-group/deepgo2/blob/main/deepgo/aminoacids.py#L11
-    _MAXLEN = 1000
     _LABELS_START_IDX = DeepGO2MigratedData._LABELS_START_IDX
 
-    def __init__(self, data_dir: str, go_branch: Literal["cc", "mf", "bp"]):
+    def __init__(
+        self, data_dir: str, go_branch: Literal["cc", "mf", "bp"], max_len: int = 1000
+    ):
         """
         Initializes the data migration object with a data directory and GO branch.
 
         Args:
             data_dir (str): Directory containing the data files.
             go_branch (Literal["cc", "mf", "bp"]): GO branch to use.
+            max_len (int): Used to truncate the sequence to this length. Default is 1000.
+                # https://github.com/bio-ontology-research-group/deepgo2/blob/main/deepgo/aminoacids.py#L11
         """
         valid_go_branches = list(DeepGO2MigratedData.GO_BRANCH_MAPPING.keys())
         if go_branch not in valid_go_branches:
             raise ValueError(f"go_branch must be one of {valid_go_branches}")
         self._go_branch = go_branch
 
         self._data_dir: str = os.path.join(rf"{data_dir}", go_branch)
+        self._max_len: int = max_len
+
         self._train_df: Optional[pd.DataFrame] = None
         self._test_df: Optional[pd.DataFrame] = None
         self._validation_df: Optional[pd.DataFrame] = None
@@ -74,33 +78,61 @@ def migrate(self) -> None:
                 "Data splits or terms data is not available in instance variables."
             )
 
-        self.save_migrated_data(data_df, splits_df)
+        self.save_migrated_data(data_with_labels_df, splits_df)
 
     def _load_data(self) -> None:
         """
         Loads the test, train, validation, and terms data from the pickled files
         in the data directory.
         """
+
         try:
             print(f"Loading data from directory: {self._data_dir}......")
-            self._test_df = pd.DataFrame(
-                pd.read_pickle(os.path.join(self._data_dir, "test_data.pkl"))
+            self._test_df = self._truncate_sequences(
+                pd.DataFrame(
+                    pd.read_pickle(os.path.join(self._data_dir, "test_data.pkl"))
+                )
             )
-            self._train_df = pd.DataFrame(
-                pd.read_pickle(os.path.join(self._data_dir, "train_data.pkl"))
+            self._train_df = self._truncate_sequences(
+                pd.DataFrame(
+                    pd.read_pickle(os.path.join(self._data_dir, "train_data.pkl"))
+                )
             )
-            self._validation_df = pd.DataFrame(
-                pd.read_pickle(os.path.join(self._data_dir, "valid_data.pkl"))
+            self._validation_df = self._truncate_sequences(
+                pd.DataFrame(
+                    pd.read_pickle(os.path.join(self._data_dir, "valid_data.pkl"))
+                )
             )
+
             self._terms_df = pd.DataFrame(
                 pd.read_pickle(os.path.join(self._data_dir, "terms.pkl"))
             )
+
         except FileNotFoundError as e:
             raise FileNotFoundError(
                 f"Data file not found in directory: {e}. "
                 "Please ensure all required files are available in the specified directory."
             )
 
+    def _truncate_sequences(
+        self, df: pd.DataFrame, column: str = "sequences"
+    ) -> pd.DataFrame:
+        """
+        Truncate sequences in a specified column of a dataframe to the maximum length.
+
+        https://github.com/bio-ontology-research-group/deepgo2/blob/main/train_cnn.py#L206-L217
+
+        Args:
+            df (pd.DataFrame): The input dataframe containing the data to be processed.
+            column (str, optional): The column containing sequences to truncate.
+                Defaults to "sequences".
+
+        Returns:
+            pd.DataFrame: The dataframe with sequences truncated to `self._max_len`.
+        """
+        df[column] = df[column].apply(lambda x: x[: self._max_len])
+        return df
+
     def _record_splits(self) -> pd.DataFrame:
         """
         Creates a DataFrame that stores the IDs and their corresponding data splits.
@@ -217,7 +249,7 @@ def save_migrated_data(
         print("Saving transformed data......")
         deepgo_migr_inst: DeepGO2MigratedData = DeepGO2MigratedData(
             go_branch=DeepGO2MigratedData.GO_BRANCH_MAPPING[self._go_branch],
-            max_sequence_length=self._MAXLEN,
+            max_sequence_length=self._max_len,
         )
 
         # Save data file
@@ -257,7 +289,9 @@ class Main:
     """
 
     @staticmethod
-    def migrate(data_dir: str, go_branch: Literal["cc", "mf", "bp"]) -> None:
+    def migrate(
+        data_dir: str, go_branch: Literal["cc", "mf", "bp"], max_len: int = 1000
+    ) -> None:
         """
         Initiates the migration process by creating a DeepGoDataMigration instance
         and invoking its migrate method.
@@ -268,8 +302,10 @@ def migrate(data_dir: str, go_branch: Literal["cc", "mf", "bp"]) -> None:
                                                   ("cc" for cellular_component,
                                                    "mf" for molecular_function,
                                                    or "bp" for biological_process).
+            max_len (int): Used to truncate the sequence to this length. Default is 1000.
+                # https://github.com/bio-ontology-research-group/deepgo2/blob/main/deepgo/aminoacids.py#L11
         """
-        DeepGo2DataMigration(data_dir, go_branch).migrate()
+        DeepGo2DataMigration(data_dir, go_branch, max_len).migrate()
 
 
 if __name__ == "__main__":