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#!/usr/bin/env python

# 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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