Update plant-genomic-benchmark.py

plant-genomic-benchmark.py

@@ -4,7 +4,6 @@
 
 import os
 from typing import List
-from Bio import SeqIO
 import datasets
 
 
@@ -69,6 +68,25 @@ _TASK_INFO = {'poly_a':{'type': 'binary', 'val_set':False},
               'pro_seq':{'type':'binary','val_set':True}
               }
 
+
+# This function is a basic reimplementation of SeqIO's parse method. This allows the
+# dataset viewer to work as it does not require an external package.
+def parse_fasta(fp):
+    name, seq = None, []
+    for line in fp:
+        line = line.rstrip()
+        if line.startswith(">"):
+            if name:
+                # Slice to remove '>'
+                yield (name[1:], "".join(seq))
+            name, seq = line, []
+        else:
+            seq.append(line)
+    if name:
+        # Slice to remove '>'
+        yield (name[1:], "".join(seq))
+        
+
 class AgroNtTasksConfig(datasets.BuilderConfig):
     """BuilderConfig for the Agro NT supervised learning tasks dataset."""
 
@@ -167,24 +185,29 @@ class AgroNtTasks(datasets.GeneratorBasedBuilder):
 
     # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
     def _generate_examples(self, filepath):
-        with open(filepath, 'r') as f:
-            key = 0
-            for record in SeqIO.parse(f,'fasta'):
-                # Yields examples as (key, example) tuples
+        
+        key = 0
 
-                split_name = record.name.split("|")
+        with open(file, "rt") as f:
+            fasta_sequences = parse_fasta(f)
+        
+            for name, seq in fasta_sequences:
+                # Yields examples as (key, example) tuples
+                sequence, name = str(seq), str(name)
+                
+                split_name = name.split("|")
                 name = split_name[0]
                 labels = split_name[1:]
 
                 if 'multi' in self.config.task_type:
                     yield key, {
-                        "sequence": str(record.seq),
+                        "sequence": sequence,
                         "name": name,
                         "labels": labels
                     }
                 else:
                     yield key, {
-                        "sequence": str(record.seq),
+                        "sequence": sequence,
                         "name": name,
                         "label": labels[0],
                     }