annotate efetch.py @ 6:554c807c6503 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit b399ac5996d8225353d3abaff58eb986da5545d7"
author iuc
date Wed, 06 Oct 2021 07:58:26 +0000
parents b00212deaea7
children ad1e5225bca4
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68cd8d564e0a 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 glob
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5 import json
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6 import logging
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7 import os
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732a52c18758 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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10 import eutils
68cd8d564e0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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13 logging.basicConfig(level=logging.INFO)
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16 def handleEfetchException(e, db, payload):
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17 logging.error('No results returned. This could either be due to no records matching the supplied IDs for the query database or it could be an error due to invalid parameters. The reported exception was "%s".\n\nPayload used for the efetch query to database "%s"\n\n%s', e, db, json.dumps(payload, indent=4))
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19 # Create a file in the downloads folder so that the user can access run information
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20 current_directory = os.getcwd()
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21 final_directory = os.path.join(current_directory, r'downloads')
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22 if not os.path.exists(final_directory):
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23 os.makedirs(final_directory)
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25 print('The following files were downloaded:')
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26 print(os.listdir(final_directory))
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28 file_path = os.path.join('downloads', 'no_results.txt')
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29 with open(file_path, 'w') as handle:
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30 handle.write('No results')
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33 def localFetch(db, gformat, newname, **payload):
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34 problem = None
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35 try:
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36 c.fetch(db, **payload)
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38 for chunk, file in enumerate(glob.glob('downloads/EFetch *')):
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39 os.rename(file, '%s%s.%s' % (newname, chunk + 1, gformat))
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41 except Exception as e:
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42 problem = e
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43 handleEfetchException(e, db, payload)
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44 else:
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45 print('The following files were downloaded:')
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46 print(os.listdir('downloads'))
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48 return problem
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50
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51 if __name__ == '__main__':
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52 parser = argparse.ArgumentParser(description='EFetch', epilog='')
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53 parser.add_argument('db', help='Database to use')
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54 parser.add_argument('--user_email', help="User email")
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55 parser.add_argument('--admin_email', help="Admin email")
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57 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
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59 # ID source
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60 parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink')
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61 parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink')
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62 parser.add_argument('--id_list', help='list of ids')
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63 parser.add_argument('--id', help='Comma separated individual IDs')
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64 parser.add_argument('--history_file', help='Fetch results from previous query (JSON)')
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65 parser.add_argument('--history_xml', help='Fetch results from previous query (XML)')
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67 # Output
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68 parser.add_argument('--retmode', help='Retmode')
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69 parser.add_argument('--rettype', help='Rettype')
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70 parser.add_argument('--galaxy_format', help='Galaxy format')
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71 args = parser.parse_args()
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73 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
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75 payload = {}
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76 for attr in ('retmode', 'rettype'):
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77 if getattr(args, attr, None) is not None:
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78 payload[attr] = getattr(args, attr)
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79
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80 if args.history_file is not None or args.history_xml is not None:
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81 if args.history_file is not None:
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82 input_histories = c.get_histories()
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83 else:
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84 input_histories = c.extract_histories_from_xml_file(args.history_xml)
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85
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86 problem = None
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87 for hist in input_histories:
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88 qkey = hist['query_key']
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89 tmp_payload = payload
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90 tmp_payload.update(hist)
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91 newname = 'downloads/EFetch-%s-%s-querykey%s-chunk' % (args.rettype, args.retmode, qkey)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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92 problem = localFetch(args.db, args.galaxy_format, newname, **tmp_payload)
b00212deaea7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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93
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94 if os.path.exists('downloads'):
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95 os.rename('downloads', 'downloads-qkey%s' % (qkey))
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96
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97 if not os.path.exists('downloads'):
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98 os.makedirs('downloads')
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99
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100 for relpath in glob.glob('downloads-qkey*/*'):
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101 file = os.path.basename(relpath)
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102 os.rename(relpath, 'downloads/%s' % (file))
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103
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104 if problem is not None:
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105 raise(problem)
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106
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107 else:
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108 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
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109 payload['id'] = ','.join(merged_ids)
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110 newname = 'downloads/EFetch-%s-%s-chunk' % (args.rettype, args.retmode)
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111 localFetch(args.db, args.galaxy_format, newname, **payload)