Add human

oas-paired-sequence-data.py

@@ -50,7 +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"

src/oas-data-cleaning.py

@@ -53,19 +53,18 @@ for species in species_list:
         print(f"{species} output summary:")
         print(species_df.head())
         print(species_df.shape)
-        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"])
+        os.makedirs(species, exist_ok=True)
+        species_df.to_parquet(species, partition_cols=["data_unit"])
         zip_name = species + ".tar.gz"
         print(f"Creating {zip_name}")
         with tarfile.open(zip_name, "w:gz") as tf:
-            tf.add(parquet_dir)
+            tf.add(species, arcname="")
         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 {parquet_dir}")
-        shutil.rmtree(parquet_dir)
+        print(f"Removing {species}")
+        shutil.rmtree(species)
         print(f"Removing {zip_name}")
         os.remove(zip_name)