Update

ASCN_Download.py

@@ -1,9 +1,18 @@
-#!/usr/bin/env python3
-
 from Bio import Entrez
 import sys
 
+
 def fetch_sequences(database, accession_numbers):
+    """
+    Fetch sequences from NCBI database using accession numbers.
+    
+    Args:
+        database (str): Database name to fetch sequences from.
+        accession_numbers (list): List of accession numbers.
+        
+    Returns:
+        None
+    """
     Entrez.email = "fakeemail@exemplo.com"
     Entrez.tool = "fetch_sequences.py"
 
@@ -19,24 +28,47 @@ def fetch_sequences(database, accession_numbers):
         print(f"Error fetching sequences: {e}")
         sys.exit(1)
 
-if __name__ == '__main__':
-    if len(sys.argv) != 3:
-        print("Usage: python fetch_sequences.py [database] [file_path_to_accession_numbers]")
-        sys.exit(1)
-
-    database = sys.argv[1]
-    file_path = sys.argv[2]
 
+def read_accession_numbers(file_path):
+    """
+    Read accession numbers from a file.
+    
+    Args:
+        file_path (str): Path to the file containing accession numbers.
+        
+    Returns:
+        list: List of accession numbers.
+    """
     try:
         with open(file_path) as file:
             # Filter out empty lines and strip whitespace from each line
             accession_numbers = [line.strip() for line in file if line.strip()]
+        return accession_numbers
     except FileNotFoundError:
         print(f"Error: File '{file_path}' not found.")
         sys.exit(1)
 
+
+def main():
+    """
+    Main function to execute the script.
+    """
+    if len(sys.argv) != 3:
+        print("Usage: python fetch_sequences.py [database] "
+        "[file_path_to_accession_numbers]")
+        sys.exit(1)
+
+    database = sys.argv[1]
+    file_path = sys.argv[2]
+
+    accession_numbers = read_accession_numbers(file_path)
+
     if not accession_numbers:
         print("Error: No accession numbers found in the file.")
         sys.exit(1)
 
     fetch_sequences(database, accession_numbers)
+
+
+if __name__ == '__main__':
+    main()