#!/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)
