rat test

src/oas-data-cleaning.py

@@ -7,11 +7,12 @@ import boto3
 data_dir = os.getcwd()
 output_path = os.getcwd()
 
-species_list = ["human", "rat_SD", "mouse_BALB_c", "mouse_C57BL_6"]
+# species_list = ["rat_SD", "mouse_BALB_c", "mouse_C57BL_6", "human"]
+species_list = ["rat_SD"]
 
 S3_BUCKET = "aws-hcls-ml"
 S3_PREFIX = "oas-paired-sequence-data"
-s3 = boto3.client('s3')
+s3 = boto3.client("s3")
 for species in species_list:
     print(f"Downloading {species} files")
     list_of_df = []
@@ -26,7 +27,7 @@ for species in species_list:
                 header=1,
                 compression="gzip",
                 on_bad_lines="warn",
-                low_memory=False
+                low_memory=False,
             )
             run_data = run_data[
                 [
@@ -65,16 +66,13 @@ for species in species_list:
         # output_file_name = os.path.join(output_path, species + ".zip")
         output_file_name = os.path.join(output_path, "train.csv")
         print(f"Creating {output_file_name}")
-        # 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, compression="zip")
+        # species_df.to_csv(output_file_name, index=False)
         # zip_name = os.path.join(output_path, species + ".zip")
         zip_name = species + ".zip"
         with ZipFile(zip_name, "w") as myzip:
-            myzip.write('train.csv')
+            myzip.write("train.csv")
         s3.upload_file(zip_name, S3_BUCKET, os.path.join(S3_PREFIX, zip_name))
         os.remove(output_file_name)
         os.remove(zip_name)
-        
-
-