Mercurial > repos > iuc > ncbi_eutils_efetch

annotate esearch.py @ 3:c09fcbe4b16a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:48:53 +0000
parents 0fc65a60436f
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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1 #!/usr/bin/env python
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3 import argparse
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4 import json
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5 import logging
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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8 import eutils
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11 logging.basicConfig(level=logging.INFO)
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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14 if __name__ == '__main__':
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15 parser = argparse.ArgumentParser(description='ESearch', epilog='')
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16 parser.add_argument('db', help='Database to use')
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17 parser.add_argument('term', help='Query')
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18 parser.add_argument('--history_file', help='Filter existing history')
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19 parser.add_argument('--datetype', help='Date type')
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20 parser.add_argument('--reldate', help='In past N days')
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21 parser.add_argument('--mindate', help='Minimum date')
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22 parser.add_argument('--maxdate', help='maximum date')
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23 # History
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24 parser.add_argument('--history_out', action="store_true", help='Output history file')
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25 parser.add_argument('--user_email', help="User email")
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26 parser.add_argument('--admin_email', help="Admin email")
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28 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
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30 # Output
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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31 parser.add_argument('--retmode', help='Retmode')
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32 parser.add_argument('--rettype', help='Rettype')
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33 parser.add_argument('--retstart', type=int, default=0, help='Retstart - Starting rec number (0)')
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34 parser.add_argument('--retmax', type=int, default=20, help='Retmax - max number of recs returned (20, max 100000)')
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36 args = parser.parse_args()
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38 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
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40 max_retmax = 100000
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41 min_retmax = 1
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42 max = max(min(args.retmax, max_retmax), min_retmax)
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44 payload = {
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45 'db': args.db,
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46 'term': args.term,
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47 }
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48 if args.history_file is not None:
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49 payload.update(c.get_history())
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51 # if args.history_out is not None:
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52 if args.history_out:
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53 payload['usehistory'] = 'y'
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55 payload['retmode'] = args.retmode
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57 for attr in ('datetype', 'reldate', 'mindate', 'maxdate', 'rettype', 'retmax', 'retstart'):
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58 if getattr(args, attr, None) is not None:
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59 payload[attr] = getattr(args, attr)
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61 logging.info("Payload used for query:" + json.dumps(payload, indent=4))
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63 results = c.search(**payload)
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65 # We're going to infer that rettype being uilist means convert to text format (which esearch does not do)
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66 if args.retmode == 'text':
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67 ids = c.xmlstring2UIlist(results)
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68 for id in ids:
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69 print(id)
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70 elif args.retmode == 'json':
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71 json_data = c.jsonstring2jsondata(results)
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72 print(json.dumps(json_data, indent=4))
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73 else:
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74 print(results)