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#!/usr/bin/env python
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Query PubMed and print MEDLINE format results."""
import getopt
import sys
from Bio import Entrez
def print_usage():
"""Print a help message."""
print(
"""query_pubmed.py [-h] [-c] [-d delay] query
This script sends a query to PubMed (via the NCBI Entrez webservice*)
and prints the MEDLINE formatted results to the screen.
Arguments:
-h Print out this help message.
-c Count the hits, and don't print them out.
* http://www.ncbi.nlm.nih.gov/Entrez/
"""
)
if __name__ == "__main__":
try:
optlist, args = getopt.getopt(sys.argv[1:], "hcd:")
except getopt.error as x:
print(x)
sys.exit(0)
if len(args) != 1: # If they gave extraneous arguments,
print_usage() # print the instructions and quit.
sys.exit(0)
query = args[0]
show_help = False
count_only = False
for opt, arg in optlist:
if opt == "-h":
show_help = True
elif opt == "-c":
count_only = True
elif opt == "-d":
sys.stderr.write("The delay parameter is now ignored\n")
if show_help:
print_usage()
sys.exit(0)
print("Doing a PubMed search for %r..." % query)
if count_only:
handle = Entrez.esearch(db="pubmed", term=query)
else:
handle = Entrez.esearch(db="pubmed", term=query, usehistory="Y")
search_results = Entrez.read(handle)
ids = search_results["IdList"]
count = len(ids)
print(f"Found {count:d} citations")
if count_only:
sys.exit(0)
webenv = search_results["WebEnv"]
query_key = search_results["QueryKey"]
batch_size = 3
for start in range(0, count, batch_size):
end = min(count, start + batch_size)
# print("Going to download record %i to %i" % (start+1, end))
fetch_handle = Entrez.efetch(
db="pubmed",
rettype="medline",
retmode="text",
retstart=start,
retmax=batch_size,
webenv=webenv,
query_key=query_key,
)
data = fetch_handle.read()
fetch_handle.close()
sys.stdout.write(data)
sys.stdout.flush()
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