cleanup

oas-paired-sequence-data.py

@@ -3,9 +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 pandas as pd
 import datasets
+import pandas as pd
 import os
 
 _CITATION = """\
@@ -24,19 +23,16 @@ 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/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",    
+    "mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.tar.gz",
 }
 _FEATURES = datasets.Features(
     {
-        # "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"),
@@ -45,18 +41,6 @@ _FEATURES = datasets.Features(
         "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"),
     }
 )
 
@@ -66,7 +50,7 @@ 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"
@@ -92,13 +76,11 @@ 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),
                     "split": "train",
                 },
             ),
         ]
-    
 
     def _generate_examples(self, filepath, split):
         table = pd.read_parquet(filepath)
@@ -106,8 +88,6 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
             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],
@@ -118,34 +98,3 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
                 "cdr3_aa_light": row[8],
             }
 
-
-    # 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],
-    #             }
-

src/oas-data-cleaning.py

@@ -1,18 +1,15 @@
+import boto3
+import io
 import os
 import pandas as pd
 import re
-
-# from zipfile import ZipFile
-import tarfile
-import boto3
-import io
 import shutil
+import tarfile
 
 data_dir = os.getcwd()
 output_path = os.getcwd()
 
-# species_list = ["rat_SD", "mouse_BALB_c", "mouse_C57BL_6", "human"]
-species_list = ["human"]
+species_list = ["rat_SD", "mouse_BALB_c", "mouse_C57BL_6", "human"]
 
 S3_BUCKET = "aws-hcls-ml"
 S3_SRC_PREFIX = "oas-paired-sequence-data/raw"
@@ -50,40 +47,23 @@ for species in species_list:
                 ]
             ]
             run_data = run_data.dropna()
-            # run_data = run_data.apply(calc_cdr_coordinates, axis=1)
-            # run_data.insert(
-            #     0, "pair_id", run_id + "_" + run_data.reset_index().index.map(str)
-            # )
             run_data.insert(0, "data_unit", run_id)
             list_of_df.append(run_data)
         species_df = pd.concat(list_of_df, ignore_index=True)
         print(f"{species} output summary:")
         print(species_df.head())
         print(species_df.shape)
-        # output_file_name = os.path.join(output_path, "train.csv")
-        # output_file_name = os.path.join(output_path, "train.parquet")
-        # print(f"Creating {output_file_name}")
         parquet_dir = os.path.join(output_path, species)
         os.makedirs(parquet_dir, exist_ok=True)
         species_df.to_parquet(parquet_dir, partition_cols=["data_unit"])
-        # species_df.to_csv(output_file_name, index=False, compression="zip")
-        # species_df.to_csv(output_file_name, index=False)
-        # species_df.to_csv(output_file_name, index=False)
-        # zip_name = species + ".zip"
         zip_name = species + ".tar.gz"
         print(f"Creating {zip_name}")
-        # with ZipFile(zip_name, "w") as myzip:
-        #     myzip.write("train.csv")
-
         with tarfile.open(zip_name, "w:gz") as tf:
-            # tf.add("train.csv")
             tf.add(parquet_dir)
         print(
             f"Uploading {zip_name} to {os.path.join('s3://', S3_BUCKET, S3_DEST_PREFIX)}"
         )
         s3.upload_file(zip_name, S3_BUCKET, os.path.join(S3_DEST_PREFIX, zip_name))
-        # print(f"Removing {output_file_name}")
-        # os.remove(output_file_name)
         print(f"Removing {parquet_dir}")
         shutil.rmtree(parquet_dir)
         print(f"Removing {zip_name}")