1-fix-dataset-preview

nucleotide_transformer_downstream_tasks.py

@@ -18,7 +18,25 @@ Transformer paper."""
 from typing import List
 
 import datasets
-from Bio import SeqIO
+
+
+# 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))
+
 
 # Find for instance the citation on arxiv or on the dataset repo/website
 _CITATION = """\
@@ -131,12 +149,12 @@ class NucleotideTransformerDownstreamTasks(datasets.GeneratorBasedBuilder):
     def _generate_examples(self, file):
         key = 0
         with open(file, "rt") as f:
-            fasta_sequences = SeqIO.parse(f, "fasta")
+            fasta_sequences = parse_fasta(f)
 
-            for record in fasta_sequences:
+            for name, seq in fasta_sequences:
 
                 # parse descriptions in the fasta file
-                sequence, name = str(record.seq), str(record.name)
+                sequence, name = str(seq), str(name)
                 label = int(name.split("|")[-1])
 
                 # yield example