update

oas-paired-sequence-data.py

@@ -90,8 +90,7 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    # "filepath": os.path.join(data_dir, "train.csv"),
-                    "filepath": data_dir['train'],
+                    "filepath": os.path.join(data_dir, "train.csv"),
                     "split": "train",
                 },
             ),

src/mouse_C57BL_6.zip

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:d610083fbd6e7efb45d1675b341bd1cd375b99465f040363ce70953e6a7a46cf
-size 379666

src/oas-data-cleaning.py

@@ -1,13 +1,17 @@
 import os
 import pandas as pd
 import re
+from zipfile import ZipFile
+import boto3
 
 data_dir = os.getcwd()
 output_path = os.getcwd()
 
 species_list = ["human", "rat_SD", "mouse_BALB_c", "mouse_C57BL_6"]
 
-
+S3_BUCKET = "aws-hcls-ml"
+S3_PREFIX = "oas-paired-sequence-data"
+s3 = boto3.client('s3')
 for species in species_list:
     print(f"Downloading {species} files")
     list_of_df = []
@@ -50,18 +54,6 @@ for species in species_list:
                 return row
 
             run_data = run_data.apply(calc_cdr_coordinates, axis=1)
-
-            # run_data = run_data.drop(
-            #     columns=[
-            #         "cdr1_aa_heavy",
-            #         "cdr2_aa_heavy",
-            #         "cdr3_aa_heavy",
-            #         "cdr1_aa_light",
-            #         "cdr2_aa_light",
-            #         "cdr3_aa_light",
-            #     ]
-            # )
-
             run_data.insert(
                 0, "pair_id", run_id + "_" + run_data.reset_index().index.map(str)
             )
@@ -70,7 +62,19 @@ for species in species_list:
         print(f"{species} output summary:")
         print(species_df.head())
         print(species_df.shape)
-        output_file_name = os.path.join(output_path, species + ".zip")
+        # 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, 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')
+        s3.upload_file(zip_name, S3_BUCKET, os.path.join(S3_PREFIX, zip_name))
+        os.remove(output_file_name)
+        os.remove(zip_name)
+        
+
+
 

src/train.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:bdffac439366acf3043668b2242cfe2e533dd37e2a6fac78fbaea6eb1a45f0ca
-size 379714