try parquet

oas-paired-sequence-data.py

@@ -3,7 +3,8 @@
 # Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
 # SPDX-License-Identifier: MIT-0
 """Paired sequences from the Observed Antibody Space database"""
-import csv
+# import csv
+import pandas as pd
 import datasets
 import os
 
@@ -23,17 +24,19 @@ Paired heavy and light chain antibody sequences for multiple species.
 _HOMEPAGE = "https://opig.stats.ox.ac.uk/webapps/oas/"
 
 _LICENSE = "cc-by-4.0"
-_BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/processed/"
+# _BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/processed/"
+_BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/parquet/"
+
 _URLS = {
-    "human": _BASE_URL + "human.tar.gz",
+    # "human": _BASE_URL + "human.tar.gz",
     "rat_SD": _BASE_URL + "rat_SD.tar.gz",
     "mouse_BALB_c": _BASE_URL + "mouse_BALB_c.tar.gz",
     "mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.tar.gz",    
 }
-
 _FEATURES = datasets.Features(
     {
-        "pair_id": datasets.Value("string"),
+        # "pair_id": datasets.Value("string"),
+        "data_unit": datasets.Value("string"),
         "sequence_alignment_aa_heavy": datasets.Value("string"),
         "cdr1_aa_heavy": datasets.Value("string"),
         "cdr2_aa_heavy": datasets.Value("string"),
@@ -63,7 +66,7 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
 
     VERSION = datasets.Version("1.2.0")
     BUILDER_CONFIGS = [
-        datasets.BuilderConfig(name="human", version=VERSION, description="Human"),
+        # datasets.BuilderConfig(name="human", version=VERSION, description="Human"),
         datasets.BuilderConfig(name="rat_SD", version=VERSION, description="rat_SD"),
         datasets.BuilderConfig(
             name="mouse_BALB_c", version=VERSION, description="mouse_BALB_c"
@@ -89,39 +92,72 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "filepath": os.path.join(data_dir, "train.csv"),
+                    # "filepath": os.path.join(data_dir, "train.csv"),
+                    "filepath": os.path.join(data_dir),
                     "split": "train",
                 },
             ),
         ]
+    
 
     def _generate_examples(self, filepath, split):
-        with open(filepath, newline="") as f:
-            reader = csv.reader(f, delimiter=",")
-            for key, row in enumerate(reader):
-                if key == 0:
-                    continue
-                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],
-                    # "cdr1_aa_heavy_start": row[9],
-                    # "cdr1_aa_heavy_end": row[10],
-                    # "cdr1_aa_light_start": row[11],
-                    # "cdr1_aa_light_end": row[12],
-                    # "cdr2_aa_heavy_start": row[13],
-                    # "cdr2_aa_heavy_end": row[14],
-                    # "cdr2_aa_light_start": row[15],
-                    # "cdr2_aa_light_end": row[16],
-                    # "cdr3_aa_heavy_start": row[17],
-                    # "cdr3_aa_heavy_end": row[18],
-                    # "cdr3_aa_light_start": row[19],
-                    # "cdr3_aa_light_end": row[20],
-                }
+        table = pd.read_parquet(filepath)
+        for key, row in enumerate(table.itertuples()):
+            if key == 0:
+                continue
+            yield key, {
+                # "pair_id": row[0],
+                "data_unit": 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],
+                # "cdr1_aa_heavy_start": row[9],
+                # "cdr1_aa_heavy_end": row[10],
+                # "cdr1_aa_light_start": row[11],
+                # "cdr1_aa_light_end": row[12],
+                # "cdr2_aa_heavy_start": row[13],
+                # "cdr2_aa_heavy_end": row[14],
+                # "cdr2_aa_light_start": row[15],
+                # "cdr2_aa_light_end": row[16],
+                # "cdr3_aa_heavy_start": row[17],
+                # "cdr3_aa_heavy_end": row[18],
+                # "cdr3_aa_light_start": row[19],
+                # "cdr3_aa_light_end": row[20],
+            }
+
+
+    # def _generate_examples(self, filepath, split):
+    #     with open(filepath, newline="") as f:
+    #         reader = csv.reader(f, delimiter=",")
+    #         for key, row in enumerate(reader):
+    #             if key == 0:
+    #                 continue
+    #             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],
+    #                 # "cdr1_aa_heavy_start": row[9],
+    #                 # "cdr1_aa_heavy_end": row[10],
+    #                 # "cdr1_aa_light_start": row[11],
+    #                 # "cdr1_aa_light_end": row[12],
+    #                 # "cdr2_aa_heavy_start": row[13],
+    #                 # "cdr2_aa_heavy_end": row[14],
+    #                 # "cdr2_aa_light_start": row[15],
+    #                 # "cdr2_aa_light_end": row[16],
+    #                 # "cdr3_aa_heavy_start": row[17],
+    #                 # "cdr3_aa_heavy_end": row[18],
+    #                 # "cdr3_aa_light_start": row[19],
+    #                 # "cdr3_aa_light_end": row[20],
+    #             }