add data and script

README.md

@@ -1,3 +1,20 @@
+---
+annotations_creators:
+- found
+language:
+- en
+license: mit
+multilinguality: monolingual
+pretty_name: vep_clinvar_chr1_split
+size_categories:
+- 10K<n<100K
+source_datasets:
+- original
+task_categories:
+- sequence-modeling
+task_ids:
+- sequence-classification
+---
 # vep_clinvar_chr1_split
 
 - 字段: ref, alt, label, chromosome, position

test.csv

@@ -1,4 +1,4 @@
-chrom,pos,ref,alt,label
+chromosome,position,ref,alt,label
 1,69511,A,G,False
 1,953279,T,C,False
 1,973858,G,C,False

train.csv

@@ -1,4 +1,4 @@
-chrom,pos,ref,alt,label
+chromosome,position,ref,alt,label
 2,45695,C,G,True
 2,45696,C,G,True
 2,272203,C,T,False

vep_clinvar_chr1_split.py

@@ -22,8 +22,8 @@ class VepClinvarChr1Split(GeneratorBasedBuilder):
                 "ref_forward_sequence": Value("string"),
                 "alt_forward_sequence": Value("string"),
                 "label": Value("int64"),
-                "chrom": Value("string"),
-                "pos": Value("int64"),
+                "chromosome": Value("string"),
+                "position": Value("int64"),
                 "ref": Value("string"),
                 "alt": Value("string"),
             }
@@ -44,10 +44,10 @@ class VepClinvarChr1Split(GeneratorBasedBuilder):
             raise ValueError("You must provide fasta_path when loading the dataset!")
         fasta = Fasta(fasta_path)
         for idx, row in df.iterrows():
-            chrom = str(row['chrom'])
+            chrom = str(row['chromosome'])
             if not chrom.startswith('chr'):
                 chrom = 'chr' + chrom
-            pos = row['pos']
+            pos = row['position']
             ref = row['ref']
             alt = row['alt']
             half = seq_len // 2
@@ -66,8 +66,8 @@ class VepClinvarChr1Split(GeneratorBasedBuilder):
                 "ref_forward_sequence": ref_seq,
                 "alt_forward_sequence": alt_seq,
                 "label": row["label"],
-                "chrom": row["chrom"],
-                "pos": row["pos"],
+                "chromosome": row["chromosome"],
+                "position": row["position"],
                 "ref": row["ref"],
                 "alt": row["alt"]
             }