Update multi_sp.py

multi_sp.py

@@ -171,42 +171,45 @@ class MultiSpeciesGenomes(datasets.GeneratorBasedBuilder):
         for file in files:
             with open(file, 'rt') as f:
                 fasta_sequences = SeqIO.parse(f, 'fasta')
-
-                for record in fasta_sequences:
-
-                    # parse descriptions in the fasta file
-                    sequence, description = str(record.seq), record.description
-
-                    # clean chromosome sequence
-                    sequence = clean_sequence(sequence)
-                    seq_length = len(sequence)
-
-                    # split into chunks
-                    num_chunks = (seq_length - 2 * self.config.overlap) // chunk_length
-
-                    if num_chunks < 1:
-                        continue
-
-                    sequence = sequence[:(chunk_length * num_chunks + 2 * self.config.overlap)]
-                    seq_length = len(sequence)
-                    num_chunks = list(range(num_chunks))
-                    if split == 'validation':
-                        random.seed(42)
-                        random.shuffle(num_chunks)
-                        n_samples = int(len(num_chunks)*0.1)
-                        num_chunks = num_chunks[:n_samples]
-                    for i in num_chunks:
-                        # get chunk
-                        start_pos = i * chunk_length
-                        end_pos = min(seq_length, (i+1) * chunk_length + 2 * self.config.overlap)
-                        chunk_sequence = sequence[start_pos:end_pos]
-
-                        # yield chunk
-                        yield key, {
-                            'sequence': chunk_sequence,
-                            'description': description,
-                            'start_pos': start_pos,
-                            'end_pos': end_pos,
-                            'fasta_url': file.split('::')[-1]
-                        }
-                        key += 1
+                try:
+                    for record in fasta_sequences:
+
+                        # parse descriptions in the fasta file
+                        sequence, description = str(record.seq), record.description
+
+                        # clean chromosome sequence
+                        sequence = clean_sequence(sequence)
+                        seq_length = len(sequence)
+
+                        # split into chunks
+                        num_chunks = (seq_length - 2 * self.config.overlap) // chunk_length
+
+                        if num_chunks < 1:
+                            continue
+
+                        sequence = sequence[:(chunk_length * num_chunks + 2 * self.config.overlap)]
+                        seq_length = len(sequence)
+                        num_chunks = list(range(num_chunks))
+                        if split == 'validation':
+                            random.seed(42)
+                            random.shuffle(num_chunks)
+                            n_samples = int(len(num_chunks)*0.2)
+                            num_chunks = num_chunks[:n_samples]
+                        for i in num_chunks:
+                            # get chunk
+                            start_pos = i * chunk_length
+                            end_pos = min(seq_length, (i+1) * chunk_length + 2 * self.config.overlap)
+                            chunk_sequence = sequence[start_pos:end_pos]
+
+                            # yield chunk
+                            yield key, {
+                                'sequence': chunk_sequence,
+                                'description': description,
+                                'start_pos': start_pos,
+                                'end_pos': end_pos,
+                                'fasta_url': file.split('::')[-1]
+                            }
+                            key += 1
+                except Exception as e:
+                    print(f"Error while processing {file}: {e}")
+                    continue