tar.gz

oas-paired-sequence-data.py

@@ -25,11 +25,14 @@ _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/"
 _URLS = {
-    # "human": _BASE_URL + "human.zip",
+    # "human": _BASE_URL + "human.zip",    
+    # "rat_SD": _BASE_URL + "rat_SD.zip",
+    # "mouse_BALB_c": _BASE_URL + "mouse_BALB_c.zip",
+    # "mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.zip",
     "human": _BASE_URL + "test.tar.gz",
-    "rat_SD": _BASE_URL + "rat_SD.zip",
-    "mouse_BALB_c": _BASE_URL + "mouse_BALB_c.zip",
-    "mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.zip",
+    "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(

src/oas-data-cleaning.py

@@ -1,7 +1,9 @@
 import os
 import pandas as pd
 import re
-from zipfile import ZipFile
+
+# from zipfile import ZipFile
+import tarfile
 import boto3
 import io
 
@@ -9,7 +11,7 @@ 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"]
 
 S3_BUCKET = "aws-hcls-ml"
 S3_SRC_PREFIX = "oas-paired-sequence-data/raw"
@@ -73,10 +75,14 @@ for species in species_list:
         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)
-        zip_name = species + ".zip"
+        # 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 ZipFile(zip_name, "w") as myzip:
+        #     myzip.write("train.csv")
+
+        with tarfile.open(zip_name, "w:gz") as tf:
+            tf.add("train.csv")
         print(
             f"Uploading {zip_name} to {os.path.join('s3://', S3_BUCKET, S3_DEST_PREFIX)}"
         )