single-file parquet

.gitattributes

@@ -58,3 +58,7 @@ mouse_BALB_c.zip filter=lfs diff=lfs merge=lfs -text
 mouse_C57BL_6.zip filter=lfs diff=lfs merge=lfs -text
 rat_SD.zip filter=lfs diff=lfs merge=lfs -text
 human.zip filter=lfs diff=lfs merge=lfs -text
+human.parquet filter=lfs diff=lfs merge=lfs -text
+mouse_BALB_c.parquet filter=lfs diff=lfs merge=lfs -text
+mouse_C57BL_6.parquet filter=lfs diff=lfs merge=lfs -text
+rat_SD.parquet filter=lfs diff=lfs merge=lfs -text

README.md

@@ -4,7 +4,17 @@ language: en
 task_categories:
 - fill-mask
 license: cc-by-4.0
+configs:
+- config_name: human
+  data_files: "human.parquet"
+- config_name: rat_SD
+  data_files: "rat_SD.parquet"
+- config_name: mouse_BALB_c
+  data_files: "mouse_BALB_c.parquet"
+- config_name: mouse_C57BL_6
+  data_files: "mouse_C57BL_6.parquet"
 ---
+
 # Dataset Card for OAS Paired Sequence Data
 
 ## Dataset Description

human.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:15f68167648ede70b384eb9671c162617a251bf47ce758702ce6912c2cbfe05b
+size 60616532

mouse_BALB_c.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2e0991362b6f59e1fec7751d2696db0d4ef4ab6c609a9d87d98c8ec6061df705
+size 319404

mouse_C57BL_6.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:33b0a43b2d4bcc9e24d6d1f5c747dbc9a21b4e46220da6786f0fda6e024b6f35
+size 90331

rat_SD.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1dd3a2a45f22e9e87cc13891f2db9c9e74129c23b7e8b94eda81fa1423863c40
+size 1082597

src/download_and_process_data.py

@@ -1,65 +1,41 @@
-import pandas as pd
 import os
-from datasets import load_dataset
+import pandas as pd
+import re
 
-data_dir = os.path.join(os.getcwd(), "data")
+data_dir = os.getcwd()
+output_path = os.getcwd()
 
 species_list = ["human", "rat_SD", "mouse_BALB_c", "mouse_C57BL_6"]
 
 for species in species_list:
-    species_url_file = os.path.join(os.getcwd(), species + "_oas_paired.txt")
+    print(f"Downloading {species} files")
+    species_df = pd.DataFrame(
+        columns=["run_id", "sequence_alignment_aa_heavy", "sequence_alignment_aa_light"]
+    )
+    species_url_file = os.path.join(data_dir, species + "_oas_paired.txt")
     with open(species_url_file, "r") as f:
         for csv_file in f.readlines():
             print(csv_file)
             filename = os.path.basename(csv_file)
-            filename = os.path.splitext(filename)[0]
-            filename = os.path.splitext(filename)[0]  # Not a typo, need to pull off the .gzip AND the .csv
-            df = pd.read_csv(
+            run_id = str(re.search(r"^(.*)_[Pp]aired", filename)[1])
+            run_data = pd.read_csv(
                 csv_file,
                 header=1,
                 compression="gzip",
                 on_bad_lines="warn",
             )
-            df = df[
+            run_data = run_data[
                 [
-                    "sequence_id_heavy",
-                    "sequence_heavy",
-                    "locus_heavy",
-                    "stop_codon_heavy",
-                    "productive_heavy",
-                    "rev_comp_heavy",
                     "sequence_alignment_aa_heavy",
-                    "fwr1_aa_heavy",
-                    "cdr1_aa_heavy",
-                    "fwr2_aa_heavy",
-                    "cdr2_aa_heavy",
-                    "fwr3_aa_heavy",
-                    "cdr3_aa_heavy",
-                    "junction_aa_heavy",
-                    "sequence_id_light",
-                    "sequence_light",
-                    "locus_light",
-                    "stop_codon_light",
-                    "productive_light",
-                    "rev_comp_light",
                     "sequence_alignment_aa_light",
-                    "fwr1_aa_light",
-                    "cdr1_aa_light",
-                    "fwr2_aa_light",
-                    "cdr2_aa_light",
-                    "fwr3_aa_light",
-                    "cdr3_aa_light",
-                    "junction_aa_light",
                 ]
             ]
-            df.insert(0, "run", species)
-            output_path = os.path.join(data_dir, species)
-            if not os.path.exists(output_path):
-                os.makedirs(output_path, exist_ok=True)
-            df.to_parquet(
-                os.path.join(output_path, filename + ".parquet"), compression="gzip"
-            )
-
-        x = load_dataset(output_path)
-        print(x.num_rows)
+            run_data.insert(0, "run_id", run_id)
+            species_df = pd.concat([species_df, run_data])
+        print(f"{species} output summary:")
+        print(species_df.head())
+        print(species_df.shape)
+        output_file_name = os.path.join(output_path, species + ".parquet")
+        print(f"Creating {output_file_name}")
+        species_df.to_parquet(output_file_name, compression="gzip")
 

src/human_oas_paired.txt

@@ -167,4 +167,4 @@ https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Phad_2022/csv_paired/AT7ma_S7__
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Phad_2022/csv_paired/AT7mb_S1__1_Paired_All.csv.gz
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Phad_2022/csv_paired/AT7mc_S2__1_Paired_All.csv.gz
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Phad_2022/csv_paired/AT7md_S3__1_Paired_All.csv.gz
-https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Phad_2022/csv_paired/AT7me_S4__1_Paired_All.csv.gz
+https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Phad_2022/csv_paired/AT7me_S4__1_Paired_All.csv.gz

src/mouse_BALB_c_oas_paired.txt

@@ -5,4 +5,4 @@ https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179280_p
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179283_paired.csv.gz
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179284_paired.csv.gz
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179285_paired.csv.gz
-https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179286_paired.csv.gz
+https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179286_paired.csv.gz

src/mouse_C57BL_6_oas_paired.txt

@@ -1,2 +1,2 @@
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Alsoiussi_2020/csv/SRR11528761_paired.csv.gz
-https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Alsoiussi_2020/csv/SRR11528762_paired.csv.gz
+https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Alsoiussi_2020/csv/SRR11528762_paired.csv.gz

src/rat_SD_oas_paired.txt

@@ -17,4 +17,4 @@ https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179296_p
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179297_paired.csv.gz
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179298_paired.csv.gz
 https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179299_paired.csv.gz
-https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179300_paired.csv.gz
+https://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Goldstein_2019/csv/SRR9179300_paired.csv.gz