Mercurial > repos > iuc > ncbi_eutils_efetch

annotate esummary.py @ 9:6c4b39080ed7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
author iuc
date Mon, 23 Jan 2023 10:37:57 +0000
parents c09fcbe4b16a
children
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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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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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3 import argparse
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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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4 import json
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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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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6 import os
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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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8 import eutils
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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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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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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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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14 if __name__ == '__main__':
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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15 parser = argparse.ArgumentParser(description='ESummary', epilog='')
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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16 parser.add_argument('db', help='Database to use')
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17 parser.add_argument('--user_email', help="User email")
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18 parser.add_argument('--admin_email', help="Admin email")
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20 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
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22 # ID source
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23 parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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24 parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink')
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25 parser.add_argument('--id_list', help='list of ids')
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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26 parser.add_argument('--id', help='Comma separated individual IDs')
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27 parser.add_argument('--history_file', help='Fetch results from previous query')
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28 parser.add_argument('--history_xml', help='Fetch results from previous query')
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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('--retstart', type=int, default=0, help='Retstart - Starting rec number (0)')
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33 parser.add_argument('--retmax', type=int, default=20, help='Retmax - max number of recs returned (20, max 100000')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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34
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35 args = parser.parse_args()
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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37 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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39 payload = {
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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40 'db': args.db,
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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41 }
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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42
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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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43 for attr in ('retmode', 'retmax', 'retstart'):
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44 if getattr(args, attr, None) is not None:
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45 payload[attr] = getattr(args, attr)
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47 results = []
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48 qkeys = []
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49 if args.history_file is not None or args.history_xml is not None:
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50 payload['retmode'] = args.retmode
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51 if args.history_file is not None:
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52 input_histories = c.get_histories()
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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53 else:
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54 input_histories = c.extract_histories_from_xml_file(args.history_xml)
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56 for hist in input_histories:
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57 qkeys += [hist['query_key']]
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58 tmp_payload = payload
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59 tmp_payload.update(hist)
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60 results += [c.summary(**tmp_payload)]
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61 else:
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62 # There is no uilist retmode
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63 if args.retmode == "uilist":
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64 payload['retmode'] = 'xml'
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65 else:
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66 payload['retmode'] = args.retmode
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67 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
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68 payload['id'] = ','.join(merged_ids)
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69 qkeys += [1]
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70 results += [c.summary(**payload)]
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72 # There could be multiple sets of results if a history was supplied
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73 if args.history_file is not None or args.history_xml is not None:
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74 # Multiple result sets can be returned
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75 # Create a directory for the output files
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76 current_directory = os.getcwd()
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77 final_directory = os.path.join(current_directory, r'downloads')
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78 if not os.path.exists(final_directory):
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79 os.makedirs(final_directory)
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81 logging.info("Writing files:")
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82 count = 0
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
83 if args.retmode == 'json':
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
84 for result in results:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
85 qkey = qkeys[count]
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
86 count += 1
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
87 file_path = os.path.join('downloads', '%s-querykey%s.json' % (args.db, qkey))
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
88 logging.info('%s-link%s.json' % (args.db, count))
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
89 with open(file_path, 'w') as handle:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
90 json_data = c.jsonstring2jsondata(result)
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
91 handle.write(json.dumps(json_data, indent=4))
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
92 else:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
93 for result in results:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
94 qkey = qkeys[count]
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
95 count += 1
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
96 file_path = os.path.join('downloads', '%s-querykey%s.xml' % (args.db, qkey))
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
97 logging.info('%s-link%s.xml' % (args.db, count))
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
98 with open(file_path, 'w') as handle:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
99 handle.write(result)
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
100 else:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
101 # When rettype is uilist, convert to text format (which elink does not do)
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
102 if args.retmode == 'json':
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
103 json_data = c.jsonstring2jsondata(results[0])
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
104 print(json.dumps(json_data, indent=4))
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
105 else:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
106 print(results[0])