query_pubmed.py

#!/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.

from __future__ import print_function

import sys
import getopt

from Bio import Entrez


def print_usage():
    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 %s..." % repr(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("Found %d citations" % count)

    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()