Add cdr sequences back in

oas-paired-sequence-data.py

@@ -36,7 +36,13 @@ _FEATURES = datasets.Features(
     {
         "pair_id": datasets.Value("string"),
         "sequence_alignment_aa_heavy": datasets.Value("string"),
+        "cdr1_aa_heavy": datasets.Value("string"),
+        "cdr2_aa_heavy": datasets.Value("string"),
+        "cdr3_aa_heavy": datasets.Value("string"),
         "sequence_alignment_aa_light": datasets.Value("string"),
+        "cdr1_aa_light": datasets.Value("string"),
+        "cdr2_aa_light": datasets.Value("string"),
+        "cdr3_aa_light": datasets.Value("string"),
         "cdr1_aa_heavy_start": datasets.Value("int16"),
         "cdr1_aa_heavy_end": datasets.Value("int16"),
         "cdr1_aa_light_start": datasets.Value("int16"),
@@ -99,18 +105,24 @@ class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
                 yield key, {
                     "pair_id": row[0],
                     "sequence_alignment_aa_heavy": row[1],
-                    "sequence_alignment_aa_light": row[2],
-                    "cdr1_aa_heavy_start": row[3],
-                    "cdr1_aa_heavy_end": row[4],
-                    "cdr1_aa_light_start": row[5],
-                    "cdr1_aa_light_end": row[6],
-                    "cdr2_aa_heavy_start": row[7],
-                    "cdr2_aa_heavy_end": row[8],
-                    "cdr2_aa_light_start": row[9],
-                    "cdr2_aa_light_end": row[10],
-                    "cdr3_aa_heavy_start": row[11],
-                    "cdr3_aa_heavy_end": row[12],
-                    "cdr3_aa_light_start": row[13],
-                    "cdr3_aa_light_end": row[14],
+                    "cdr1_aa_heavy": row[2],
+                    "cdr2_aa_heavy": row[3],
+                    "cdr3_aa_heavy": row[4],
+                    "sequence_alignment_aa_light": row[5],
+                    "cdr1_aa_light": row[6],
+                    "cdr2_aa_light": row[7],
+                    "cdr3_aa_light": row[8],
+                    "cdr1_aa_heavy_start": row[9],
+                    "cdr1_aa_heavy_end": row[10],
+                    "cdr1_aa_light_start": row[11],
+                    "cdr1_aa_light_end": row[12],
+                    "cdr2_aa_heavy_start": row[13],
+                    "cdr2_aa_heavy_end": row[14],
+                    "cdr2_aa_light_start": row[15],
+                    "cdr2_aa_light_end": row[16],
+                    "cdr3_aa_heavy_start": row[17],
+                    "cdr3_aa_heavy_end": row[18],
+                    "cdr3_aa_light_start": row[19],
+                    "cdr3_aa_light_end": row[20],
                 }
 

src/human.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f852475e12a5c09900863036f2f1bac0c7db055bd574baa3ee3e946742574bc8
+size 99065044

src/mouse_BALB_c.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c0581e9d410816d88b03ecbc647ecf60fa4c4f508dce5fc6dc7e57588cba411f
+size 758218

src/mouse_C57BL_6.zip

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

src/{download_and_process_data.py → oas-data-cleaning.py}

@@ -22,6 +22,7 @@ for species in species_list:
                 header=1,
                 compression="gzip",
                 on_bad_lines="warn",
+                low_memory=False
             )
             run_data = run_data[
                 [
@@ -50,16 +51,16 @@ for species in species_list:
 
             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 = 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)

src/rat_SD.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:67c37b00298bc67790e32d013891cd36d3e0404aa2d9d4d355395779807a709e
+size 2694929