add base code for deep_go data migration

- migration from deep go format to chebai->go_uniprot format

Author: aditya0by0

chebai/preprocessing/migration/deep_go_data_mirgration.py

@@ -0,0 +1,54 @@
+from typing import List
+
+import pandas as pd
+
+# https://github.com/bio-ontology-research-group/deepgo2/blob/main/deepgo/utils.py#L18-L22
+NAMESPACES = {
+    "cc": "cellular_component",
+    "mf": "molecular_function",
+    "bp": "biological_process",
+}
+
+# https://github.com/bio-ontology-research-group/deepgo2/blob/main/deepgo/aminoacids.py#L11
+MAXLEN = 1000
+
+
+def load_data(data_dir):
+    test_df = pd.DataFrame(pd.read_pickle("test_data.pkl"))
+    train_df = pd.DataFrame(pd.read_pickle("train_data.pkl"))
+    validation_df = pd.DataFrame(pd.read_pickle("valid_data.pkl"))
+
+    required_columns = [
+        "proteins",
+        "accessions",
+        "sequences",
+        # https://github.com/bio-ontology-research-group/deepgo2/blob/main/gendata/uni2pandas.py#L45-L58
+        "exp_annotations",  # Directly associated GO ids
+        # https://github.com/bio-ontology-research-group/deepgo2/blob/main/gendata/uni2pandas.py#L60-L69
+        "prop_annotations",  # Transitively associated GO ids
+    ]
+
+    new_df = pd.concat(
+        [
+            train_df[required_columns],
+            validation_df[required_columns],
+            test_df[required_columns],
+        ],
+        ignore_index=True,
+    )
+    # Generate splits.csv file to store ids of each corresponding split
+    split_assignment_list: List[pd.DataFrame] = [
+        pd.DataFrame({"id": train_df["proteins"], "split": "train"}),
+        pd.DataFrame({"id": validation_df["proteins"], "split": "validation"}),
+        pd.DataFrame({"id": test_df["proteins"], "split": "test"}),
+    ]
+
+    combined_split_assignment = pd.concat(split_assignment_list, ignore_index=True)
+
+
+def save_data(data_dir, data_df):
+    pass
+
+
+if __name__ == "__main__":
+    pass