remove urls.txt and update dataloading script

multi_species_genomes.py

@@ -19,6 +19,7 @@ from typing import List
 import datasets
 import pandas as pd
 from Bio import SeqIO
+import os
 
 
 # Find for instance the citation on arxiv or on the dataset repo/website
@@ -128,17 +129,17 @@ class MultiSpeciesGenomes(datasets.GeneratorBasedBuilder):
 
     def _split_generators(self, dl_manager: datasets.DownloadManager) -> List[datasets.SplitGenerator]:
 
-        urls_filepath = dl_manager.download_and_extract('urls.txt')
-        with open(urls_filepath) as urls_file:
-            urls = [line.rstrip() for line in urls_file]
+        genome_file_paths = dl_manager.download_and_extract('genomes.txt')
+        with open(genome_file_paths) as genome_files:
+            genomes = [os.path.join('genomes',line.rstrip()) for line in genome_files]
         
-        test_urls = urls[-50:]   # 50 genomes for test set
-        validation_urls = urls[-100:-50]  # 50 genomes for validation set
-        train_urls = urls[:-100]  # 800 genomes for training
+        test_genomes = genomes[-50:]   # 50 genomes for test set
+        validation_genomes = genomes[-100:-50]  # 50 genomes for validation set
+        train_genomes = genomes[:-100]  # 800 genomes for training
 
-        train_downloaded_files = dl_manager.download_and_extract(train_urls)
-        test_downloaded_files = dl_manager.download_and_extract(test_urls)
-        validation_downloaded_files = dl_manager.download_and_extract(validation_urls)
+        train_downloaded_files = dl_manager.download_and_extract(train_genomes)
+        test_downloaded_files = dl_manager.download_and_extract(test_genomes)
+        validation_downloaded_files = dl_manager.download_and_extract(validation_genomes)
 
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"files": train_downloaded_files, "chunk_length": self.config.chunk_length}),