https://bioinformaticsonline.com/snippets/view/43000/python-script-to-download-covid-genome? https://bioinformaticsonline.com/snippets/view/43000/python-script-to-download-covid-genome Fri, 26 Mar 2021 07:01:29 -0500 https://bioinformaticsonline.com/snippets/view/43000/python-script-to-download-covid-genome #!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import requests import yaml seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text) seqs = seqs['genbank-sequences'] print("got %d sequences" % len(seqs)) from Bio import Entrez allseq = {} for x in seqs: if 'gene-region' in x and x['gene-region'] == "complete": nm = x['accession'] print("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().split("\n")[1:] allseq[nm] = ''.join(dna) import json with open("data/allseq.json", "w") as f: json.dump(allseq, f)]]> Surabhi Chaudhary