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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
90 lines
2.4 KiB
Python
Executable File
90 lines
2.4 KiB
Python
Executable File
#!/usr/bin/env python
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# Copyright 2000 by Jeffrey Chang. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Query PubMed and print MEDLINE format results."""
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import getopt
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import sys
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from Bio import Entrez
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def print_usage():
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"""Print a help message."""
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print(
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"""query_pubmed.py [-h] [-c] [-d delay] query
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This script sends a query to PubMed (via the NCBI Entrez webservice*)
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and prints the MEDLINE formatted results to the screen.
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Arguments:
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-h Print out this help message.
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-c Count the hits, and don't print them out.
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* http://www.ncbi.nlm.nih.gov/Entrez/
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"""
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)
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if __name__ == "__main__":
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try:
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optlist, args = getopt.getopt(sys.argv[1:], "hcd:")
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except getopt.error as x:
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print(x)
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sys.exit(0)
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if len(args) != 1: # If they gave extraneous arguments,
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print_usage() # print the instructions and quit.
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sys.exit(0)
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query = args[0]
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show_help = False
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count_only = False
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for opt, arg in optlist:
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if opt == "-h":
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show_help = True
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elif opt == "-c":
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count_only = True
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elif opt == "-d":
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sys.stderr.write("The delay parameter is now ignored\n")
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if show_help:
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print_usage()
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sys.exit(0)
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print("Doing a PubMed search for %r..." % query)
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if count_only:
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handle = Entrez.esearch(db="pubmed", term=query)
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else:
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handle = Entrez.esearch(db="pubmed", term=query, usehistory="Y")
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search_results = Entrez.read(handle)
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ids = search_results["IdList"]
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count = len(ids)
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print(f"Found {count:d} citations")
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if count_only:
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sys.exit(0)
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webenv = search_results["WebEnv"]
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query_key = search_results["QueryKey"]
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batch_size = 3
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for start in range(0, count, batch_size):
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end = min(count, start + batch_size)
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# print("Going to download record %i to %i" % (start+1, end))
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fetch_handle = Entrez.efetch(
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db="pubmed",
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rettype="medline",
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retmode="text",
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retstart=start,
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retmax=batch_size,
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webenv=webenv,
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query_key=query_key,
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)
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data = fetch_handle.read()
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fetch_handle.close()
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sys.stdout.write(data)
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sys.stdout.flush()
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