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#!/usr/bin/env python3
#
# bulk download genbank data and matadata, preparing the FASTA and the
# YAML files
#
# update-from-genbank.py --max 10 --ids ids.txt --out ~/tmp/genbank-xml
#
# See also directory .guix-run and README.md
import argparse
import gzip
import os
import sys
from utils import chunks
from Bio import Entrez
Entrez.email = 'another_email@gmail.com' # FIXME
BATCH=100
parser = argparse.ArgumentParser()
parser.add_argument('--max', type=int, help='Max queries', required=False)
parser.add_argument('--ids', type=str, help='File with ids to fetch, 1 id per line', required=True)
parser.add_argument('--out', type=str, help='Directory to write to', required=True)
args = parser.parse_args()
ids = set()
with open(args.ids) as f:
content = f.readlines()
for line in content:
ids.add(line.strip())
dir = args.out
if not os.path.exists(dir):
raise Exception(f"Directory {dir} does not exist")
request_num = BATCH
if args.max:
request_num = min(BATCH,args.max)
for i, idsx in enumerate(chunks(list(ids), request_num)):
xmlfn = os.path.join(dir, f"metadata_{i}.xml.gz")
print(f"Fetching {xmlfn} ({i*request_num})",file=sys.stderr)
with gzip.open(xmlfn, 'w') as f:
f.write((Entrez.efetch(db='nuccore', id=idsx, retmode='xml').read()).encode())
if args.max and i*request_num >= args.max:
break
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