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Overview

GDC suggests adding viral sequences and decoys to human genome when building a reference. There are about 200 viral sequences listed here. Downloading these fasta sequences one by one can be quite tedious and prone to errors.

Download steps

We put together a python script that will download all the viral sequences to a single fasta file.

  1. Copy all the lines from here and save it to a text file.(GRCh83.d1.vd1_virus_decoy.txt)
  2. Make sure biopython library is installed in your env. If using biowulf, you can do this in a conda env 
    pip3 install biopython
  3. Before launching the python script, please add your email id for Entrez.email.

This script takes one input.

Usage: gdc_download_viral_seqs.py <virus_decoys_file>

This script filters the virus decoy file to extract the accession ids for each viral sequence. Using Entrez module these ids are queried to download the fasta sequences that are all saved to the output file viral_sequences.fasta.

#!/usr/bin/env python3

import csv
import sys
from Bio import Entrez
from Bio import SeqIO

if len(sys.argv) != 2:
    print("Usage: gdc_download_viral_seqs.py <input_file>")
    sys.exit(1)

input_file = sys.argv[1]

with open(input_file, 'r', newline='') as file:
    reader = csv.reader(file, delimiter='\t')
    cleaned_data = [row for row in reader if any(row)]

accession_ids = []

if len(cleaned_data) > 1:
    for row in cleaned_data[1:]:
        if len(row) > 2:
            value = row[2] if row[2] else (row[3] if len(row) > 3 else '')
            accession_ids.append(value)
else:
    print("The file is empty or only contains empty lines.")

# Please add your email id here
Entrez.email = "vineela.gangalapudi@nih.gov"

with open("viral_sequences.fasta", "w") as output_file:
    # Iterate over each accession ID
    for accession_id in accession_ids:
        # Fetch the sequence from NCBI
        handle = Entrez.efetch(db="nucleotide", id=accession_id, rettype="fasta", retmode="text")
        fasta_sequence = handle.read()
        handle.close()

        if fasta_sequence.strip():
            # Write the fasta sequence to the output file
            output_file.write(fasta_sequence.strip() + "\n")
        else:
            print(f"Sequence not found for accession ID: {accession_id}")

If you have any questions or would like to provide valuable additions to this page please email Vineela Gangalapudi.