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#!/usr/bin/env python3
#
# Find all genbank IDs
#
# genbank-fetch-ids.py --max 1000 --skip pubseq_ids.txt
#
# See also directory .guix-run and README.md
BATCH_SIZE=5000
import argparse
import json
import os
import requests
import sys
import xml.etree.ElementTree as ET
from datetime import date, datetime
from dateutil.parser import parse
parser = argparse.ArgumentParser()
parser.add_argument('--max', type=int, help='Max queries', required=False)
parser.add_argument('--skip', type=str, help='File with ids to skip, 1 id per line', required=False)
args = parser.parse_args()
from Bio import Entrez
Entrez.email = 'another_email@gmail.com' # FIXME
# min_acceptable_collection_date = datetime(2019, 12, 1)
today_date = date.today().strftime("%Y.%m.%d")
skip = set()
if args.skip:
with open(args.skip) as f:
content = f.readlines()
for line in content:
skip.add(line.strip())
print(f"Skip size is {len(skip)}",file=sys.stderr)
# Try to search several strings
TERMS = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]']
# Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq) starting with
PREFIX = ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']
ids = set()
for term in TERMS:
num_read = BATCH_SIZE
retstart = 0
while num_read == BATCH_SIZE:
record = Entrez.read(
Entrez.esearch(db='nuccore', term=term, idtype='acc',
retstart=retstart, retmax=BATCH_SIZE)
)
idlist = record['IdList']
new_ids = set(idlist)
num_read = len(new_ids)
print(num_read,":",idlist[0],file=sys.stderr)
retstart += num_read
new_ids.difference_update(skip) # remove skip ids
new_ids = set([id for id in new_ids if id[:2] not in PREFIX])
ids.update(new_ids) # add to total set
print(f"Term: {term} --> #{len(new_ids)} new IDs ---> Total unique IDs #{len(ids)})",file=sys.stderr)
if args.max and len(ids) > args.max:
print(f"Stopping past #{args.max} items",file=sys.stderr)
break
for id in ids:
print(id)
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