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#!/usr/bin/env python3
import argparse
import json
import os
import requests
import sys
import time
parser = argparse.ArgumentParser(description="""
Fetch metadata (JSON) from PubSeq and optionally the FASTA files. IDs
can be passed in on the command line or in a file.
""")
parser.add_argument('--fasta', action='store_true', help='Also fetch FASTA records')
parser.add_argument('--out', type=str, help='Directory to write to',
required=True)
parser.add_argument('--ids', type=str, help='File with ids', required=False)
parser.add_argument('id', nargs='*', help='id(s)')
args = parser.parse_args()
dir = args.out
if not os.path.exists(dir):
raise Exception(f"Directory {dir} does not exist")
ids = args.id
if (len(ids)==0):
print(f"Reading {args.ids}")
with open(args.ids) as f:
ids = [ l.strip() for l in f.readlines() ]
for id in ids:
print(id)
jsonfn = dir+"/"+id+".json"
if not os.path.exists(jsonfn):
count = 0
r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json")
while not r:
count += 1
if count>10: raise Exception(f"Can not find record for {id}")
time.sleep(15)
r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json")
m_url = r.json()[0]['metadata']
mr = requests.get(m_url)
with open(dir+"/"+id+".json","w") as outf:
outf.write(mr.text)
if args.fasta:
fastafn = dir+"/"+id+".fa"
if os.path.exists(fastafn): continue
fa_url = r.json()[0]['fasta']
fr = requests.get(fa_url)
with open(fastafn,"w") as outf:
outf.write(fr.text)
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