Add cdr coordinates

oas-paired-sequence-data.py

@@ -36,13 +36,19 @@ _FEATURES = datasets.Features(
     {
         "pair_id": datasets.Value("string"),
         "sequence_alignment_aa_heavy": datasets.Value("string"),
-        "cdr1_aa_heavy": datasets.Value("string"),
-        "cdr2_aa_heavy": datasets.Value("string"),
-        "cdr3_aa_heavy": datasets.Value("string"),
         "sequence_alignment_aa_light": datasets.Value("string"),
-        "cdr1_aa_light": datasets.Value("string"),
-        "cdr2_aa_light": datasets.Value("string"),
-        "cdr3_aa_light": datasets.Value("string"),
+        "cdr1_aa_heavy_start": datasets.Value("int16"),
+        "cdr1_aa_heavy_end": datasets.Value("int16"),
+        "cdr1_aa_light_start": datasets.Value("int16"),
+        "cdr1_aa_light_end": datasets.Value("int16"),
+        "cdr2_aa_heavy_start": datasets.Value("int16"),
+        "cdr2_aa_heavy_end": datasets.Value("int16"),
+        "cdr2_aa_light_start": datasets.Value("int16"),
+        "cdr2_aa_light_end": datasets.Value("int16"),
+        "cdr3_aa_heavy_start": datasets.Value("int16"),
+        "cdr3_aa_heavy_end": datasets.Value("int16"),
+        "cdr3_aa_light_start": datasets.Value("int16"),
+        "cdr3_aa_light_end": datasets.Value("int16"),
     }
 )
 
@@ -93,12 +99,18 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
                 yield key, {
                     "pair_id": row[0],
                     "sequence_alignment_aa_heavy": row[1],
-                    "cdr1_aa_heavy": row[2],
-                    "cdr2_aa_heavy": row[3],
-                    "cdr3_aa_heavy": row[4],
-                    "sequence_alignment_aa_light": row[5],
-                    "cdr1_aa_light": row[6],
-                    "cdr2_aa_light": row[7],
-                    "cdr3_aa_light": row[8],
+                    "sequence_alignment_aa_light": row[2],
+                    "cdr1_aa_heavy_start": row[3],
+                    "cdr1_aa_heavy_end": row[4],
+                    "cdr1_aa_light_start": row[5],
+                    "cdr1_aa_light_end": row[6],
+                    "cdr2_aa_heavy_start": row[7],
+                    "cdr2_aa_heavy_end": row[8],
+                    "cdr2_aa_light_start": row[9],
+                    "cdr2_aa_light_end": row[10],
+                    "cdr3_aa_heavy_start": row[11],
+                    "cdr3_aa_heavy_end": row[12],
+                    "cdr3_aa_light_start": row[13],
+                    "cdr3_aa_light_end": row[14],
                 }
 

src/download_and_process_data.py

@@ -7,6 +7,7 @@ output_path = os.getcwd()
 
 species_list = ["human", "rat_SD", "mouse_BALB_c", "mouse_C57BL_6"]
 
+
 for species in species_list:
     print(f"Downloading {species} files")
     list_of_df = []
@@ -34,6 +35,32 @@ for species in species_list:
                     "cdr3_aa_light",
                 ]
             ]
+            run_data = run_data.dropna()
+
+            def calc_cdr_coordinates(row):
+                for i in range(1, 4):
+                    for j in ["heavy", "light"]:
+                        row[f"cdr{i}_aa_{j}_start"] = row[
+                            f"sequence_alignment_aa_{j}"
+                        ].find(row[f"cdr{i}_aa_{j}"])
+                        row[f"cdr{i}_aa_{j}_end"] = row[f"cdr{i}_aa_{j}_start"] + len(
+                            row[f"cdr{i}_aa_{j}"]
+                        )
+                return row
+
+            run_data = run_data.apply(calc_cdr_coordinates, axis=1)
+
+            run_data = run_data.drop(
+                columns=[
+                    "cdr1_aa_heavy",
+                    "cdr2_aa_heavy",
+                    "cdr3_aa_heavy",
+                    "cdr1_aa_light",
+                    "cdr2_aa_light",
+                    "cdr3_aa_light",
+                ]
+            )
+
             run_data.insert(
                 0, "pair_id", run_id + "_" + run_data.reset_index().index.map(str)
             )
@@ -42,7 +69,7 @@ for species in species_list:
         print(f"{species} output summary:")
         print(species_df.head())
         print(species_df.shape)
-        output_file_name = os.path.join(output_path, species + ".csv")
+        output_file_name = os.path.join(output_path, species + ".zip")
         print(f"Creating {output_file_name}")
-        species_df.to_csv(output_file_name, index=False)
+        species_df.to_csv(output_file_name, index=False, compression="zip")