Update app.py

app.py

@@ -1,4 +1,3 @@
-import streamlit as st
 import requests
 
 def get_genome_from_ncbi(accession_number):
@@ -9,7 +8,7 @@ def get_genome_from_ncbi(accession_number):
     if response.status_code == 200:
         return response.text
     else:
-        st.error("Failed to retrieve genome. Please check the accession number.")
+        print(f"Failed to retrieve genome for {accession_number}. Please check the accession number.")
         return None
 
 def extract_sequences(genome_data):
@@ -24,26 +23,36 @@ def extract_sequences(genome_data):
     return start_sequence, end_sequence
 
 def main():
-    st.title("Download Genome from NCBI")
-    st.write("Enter the accession number to download the corresponding genome.")
-
-    accession_number = st.text_input("Accession Number")
-
-    if st.button("Get Genome"):
-        if accession_number:
-            genome_data = get_genome_from_ncbi(accession_number)
-            if genome_data:
-                start_sequence, end_sequence = extract_sequences(genome_data)
-
-                # Display the sequences
-                st.text_area("Starting 55 Base Pairs", start_sequence, height=50)
-                st.text_area("Ending 114 Base Pairs", end_sequence, height=100)
-
-                # Prepare content for download
-                download_content = f"Starting 55 Base Pairs:\n{start_sequence}\n\nEnding 114 Base Pairs:\n{end_sequence}\n"
-                st.download_button("Download Sequences", download_content, file_name=f"{accession_number}_sequences.txt", mime="text/plain")
-        else:
-            st.warning("Please enter an accession number.")
+    # Read accession numbers from a text file
+    input_file = "accession_numbers.txt"  # Input file containing accession numbers
+    output_start_file = "starting_sequences.txt"  # Output file for starting 55 base pairs
+    output_end_file = "ending_sequences.txt"  # Output file for ending 114 base pairs
+
+    with open(input_file, 'r') as file:
+        accession_numbers = file.read().splitlines()  # Read lines into a list
+
+    # Prepare lists to store sequences
+    starting_sequences = []
+    ending_sequences = []
+
+    for accession_number in accession_numbers:
+        genome_data = get_genome_from_ncbi(accession_number)
+        if genome_data:
+            start_sequence, end_sequence = extract_sequences(genome_data)
+            starting_sequences.append(f"{accession_number}: {start_sequence}")
+            ending_sequences.append(f"{accession_number}: {end_sequence}")
+
+    # Write starting sequences to file
+    with open(output_start_file, 'w') as file:
+        for seq in starting_sequences:
+            file.write(seq + '\n')
+
+    # Write ending sequences to file
+    with open(output_end_file, 'w') as file:
+        for seq in ending_sequences:
+            file.write(seq + '\n')
+
+    print(f"Sequences extracted and saved to {output_start_file} and {output_end_file}.")
 
 if __name__ == "__main__":
     main()