Update rnacentral-non-coding-rna.py

rnacentral-non-coding-rna.py

@@ -3,30 +3,33 @@ import datasets
 from Bio import SeqIO
 import os
 import gzip
-import urllib.request
+import wget
 import logging
 import tqdm
 from collections import defaultdict
+import tempfile
 
-_CITATION = """\
-@article{the2019rnacentral,
-  title={RNAcentral: a hub of information for non-coding RNA sequences},
-  author={The RNAcentral Consortium},
-  journal={Nucleic acids research},
-  volume={47},
-  number={D1},
-  pages={D221--D229},
-  year={2019},
-  publisher={Oxford University Press}
-}
-"""
-
-_DESCRIPTION = """\
-RNAcentral corpus for pre-training, containing sequences and basic metadata.
-"""
+class RNACentralDownloader:
+    """Helper class to manage RNAcentral downloads"""
+    BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release"
+    
+    @staticmethod
+    def download_file(url: str, output_dir: str) -> str:
+        """Download a file with progress bar and return local path"""
+        os.makedirs(output_dir, exist_ok=True)
+        output_path = os.path.join(output_dir, os.path.basename(url))
+        
+        if os.path.exists(output_path):
+            logging.info(f"File already exists: {output_path}")
+            return output_path
+            
+        logging.info(f"Downloading {url} to {output_path}")
+        wget.download(url, output_path)
+        print()  # New line after wget progress bar
+        return output_path
 
 class RNACentralMinimalConfig(datasets.BuilderConfig):
-    """BuilderConfig for RNACentral minimal corpus."""
+    """BuilderConfig for RNAcentral minimal corpus."""
     def __init__(
         self,
         *args,
@@ -34,6 +37,7 @@ class RNACentralMinimalConfig(datasets.BuilderConfig):
         max_length: int = 10000,
         max_sequences: Optional[int] = None,
         include_metadata: bool = True,
+        cache_dir: Optional[str] = None,
         **kwargs,
     ):
         super().__init__(*args, **kwargs)
@@ -41,6 +45,7 @@ class RNACentralMinimalConfig(datasets.BuilderConfig):
         self.max_length = max_length
         self.max_sequences = max_sequences
         self.include_metadata = include_metadata
+        self.cache_dir = cache_dir or tempfile.gettempdir()
 
 class RNACentralMinimalCorpus(datasets.GeneratorBasedBuilder):
     """Minimal RNAcentral corpus for pre-training."""
@@ -58,6 +63,7 @@ class RNACentralMinimalCorpus(datasets.GeneratorBasedBuilder):
             max_sequences=1000000,
             include_metadata=True
         )
+        self.downloader = RNACentralDownloader()
     
     def _info(self):
         features = {
@@ -94,25 +100,21 @@ class RNACentralMinimalCorpus(datasets.GeneratorBasedBuilder):
         return rfam_families
 
     def _split_generators(self, dl_manager: datasets.DownloadManager):
-        base_url = "https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release"
-        urls = {
-            'sequences': f"{base_url}/sequences/rnacentral_active.fasta.gz",
-        }
+        # Direct download using wget instead of datasets downloader
+        sequences_url = f"{self.downloader.BASE_URL}/sequences/rnacentral_active.fasta.gz"
+        sequences_path = self.downloader.download_file(sequences_url, self.config.cache_dir)
         
-        if self.config.include_metadata:
-            urls['rfam'] = f"{base_url}/rfam/rfam_annotations.tsv.gz"
-        
-        downloaded_files = dl_manager.download(urls)
-    
         rfam_families = {}
         if self.config.include_metadata:
-            rfam_families = self._load_minimal_rfam(downloaded_files['rfam'])
+            rfam_url = f"{self.downloader.BASE_URL}/rfam/rfam_annotations.tsv.gz"
+            rfam_path = self.downloader.download_file(rfam_url, self.config.cache_dir)
+            rfam_families = self._load_minimal_rfam(rfam_path)
     
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "filepath": downloaded_files['sequences'],
+                    "filepath": sequences_path,
                     "rfam_families": rfam_families,
                     "split": "train",
                 },
@@ -120,7 +122,7 @@ class RNACentralMinimalCorpus(datasets.GeneratorBasedBuilder):
             datasets.SplitGenerator(
                 name=datasets.Split.VALIDATION,
                 gen_kwargs={
-                    "filepath": downloaded_files['sequences'],
+                    "filepath": sequences_path,
                     "rfam_families": rfam_families,
                     "split": "validation",
                 },