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import streamlit as st
import requests
def get_genome_from_ncbi(accession_number):
# Construct the URL for NCBI GenBank
url = f"https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?db=nuccore&id={accession_number}&report=fasta&retmode=text"
response = requests.get(url)
if response.status_code == 200:
return response.text
else:
st.warning(f"Failed to retrieve genome for {accession_number}. Please check the accession number.")
return None
def extract_sequences(genome_data):
# Extract the sequence part from the FASTA format
lines = genome_data.splitlines()
sequence = ''.join(lines[1:]) # Join all lines except the first (which is the header)
# Get the first 55 and last 114 base pairs
start_sequence = sequence[:55] # First 55 base pairs
end_sequence = sequence[-114:] # Last 114 base pairs
return start_sequence, end_sequence
def format_fasta(accession_number, sequence):
return f">{accession_number}\n{sequence}"
def main():
st.title("NCBI Genome Sequence Extractor")
# File uploader for the user to upload the input file
uploaded_file = st.file_uploader("Upload a text file containing accession numbers", type="txt")
if uploaded_file is not None:
# Read and split accession numbers from the uploaded file
accession_numbers = uploaded_file.read().decode("utf-8").splitlines()
# Prepare lists to store formatted 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)
formatted_start_sequence = format_fasta(accession_number, start_sequence)
formatted_end_sequence = format_fasta(accession_number, end_sequence)
starting_sequences.append(formatted_start_sequence)
ending_sequences.append(formatted_end_sequence)
# Write starting sequences to a file for download
start_sequences_text = "\n".join(starting_sequences)
st.download_button("Download Starting Sequences", start_sequences_text, file_name="starting_sequences.txt", mime="text/plain")
# Write ending sequences to a file for download
end_sequences_text = "\n".join(ending_sequences)
st.download_button("Download Ending Sequences", end_sequences_text, file_name="ending_sequences.txt", mime="text/plain")
if __name__ == "__main__":
main()
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