Update loading script

oas-paired-sequence-data.py

@@ -4,8 +4,11 @@
 # SPDX-License-Identifier: MIT-0
 """Paired sequences from the Observed Antibody Space database"""
 import datasets
-import pandas as pd
+import gzip
+
+# import pandas as pd
 import os
+import csv
 
 _CITATION = """\
 @article{Olsen_Boyles_Deane_2022, 
@@ -23,14 +26,14 @@ 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/parquet/"
+_BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/raw/"
 
-_URLS = {
-    "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",
-}
+# _URLS = {
+#     "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(
     {
         "sequence_alignment_aa_heavy": datasets.Value("string"),
@@ -50,7 +53,7 @@ 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"
@@ -69,32 +72,70 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
             citation=_CITATION,
         )
 
+    # def _split_generators(self, dl_manager):
+    #     urls = _URLS[self.config.name]
+    #     data_dir = dl_manager.download_and_extract(urls)
+    #     return [
+    #         datasets.SplitGenerator(
+    #             name=datasets.Split.TRAIN,
+    #             gen_kwargs={
+    #                 "filepath": os.path.join(data_dir),
+    #                 "split": "train",
+    #             },
+    #         ),
+    #     ]
+
+    # def _generate_examples(self, filepath, split):
+    #     table = pd.read_parquet(filepath)
+    #     for key, row in enumerate(table.itertuples()):
+    #         if key == 0:
+    #             continue
+    #         yield key, {
+    #             "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],
+    #         }
+
     def _split_generators(self, dl_manager):
-        urls = _URLS[self.config.name]
-        data_dir = dl_manager.download_and_extract(urls)
+        data_unit_file = os.path.join(
+            os.getcwd(), "data_units", self.config.name + ".txt"
+        )
+        with open(data_unit_file, "r") as f:
+            urls = [
+                os.path.join(_BASE_URL, self.config.name, line.strip()) for line in f
+            ]
+        data_files = dl_manager.download_and_extract(urls)
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "filepath": os.path.join(data_dir),
+                    "filepath": data_files,
                     "split": "train",
                 },
             ),
         ]
 
-    def _generate_examples(self, filepath, split):
-        table = pd.read_parquet(filepath)
-        for key, row in enumerate(table.itertuples()):
-            if key == 0:
-                continue
-            yield key, {
-                "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],
-            }
+    def _generate_examples(self, filepaths):
+        for filepath in filepaths:
+            with gzip.open(open(filepath, "rb"), "rt", encoding="utf-8") as f:
+                reader = csv.reader(f, delimiter=",")
+                for key, row in enumerate(reader):
+                    if key == 0:
+                        continue
+                    else:
+                        yield key - 1, {
+                            "sequence_alignment_aa_heavy": row[10],
+                            "cdr1_aa_heavy": row[35],
+                            "cdr2_aa_heavy": row[39],
+                            "cdr3_aa_heavy": row[43],
+                            "sequence_alignment_aa_light": row[100],
+                            "cdr1_aa_light": row[123],
+                            "cdr2_aa_light": row[127],
+                            "cdr3_aa_light": row[131],
+                        }