Mercurial > repos > iuc > ncbi_eutils_efetch
annotate egquery.py @ 1:0fc65a60436f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
| author | iuc | 
|---|---|
| date | Tue, 30 Oct 2018 19:08:30 -0400 | 
| parents | 71bcf87a7031 | 
| children | c09fcbe4b16a | 
| rev | line source | 
|---|---|
| 0 
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 1 #!/usr/bin/env python | 
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0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
 iuc parents: 
0diff
changeset | 2 from __future__ import print_function | 
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0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
 iuc parents: 
0diff
changeset | 3 | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 4 import argparse | 
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0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
 iuc parents: 
0diff
changeset | 5 | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 6 import eutils | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 7 | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 8 | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 9 if __name__ == '__main__': | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 10 parser = argparse.ArgumentParser(description='EGQuery', epilog='') | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 11 parser.add_argument('term', help='Query') | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 12 # | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 13 parser.add_argument('--user_email', help="User email") | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 14 parser.add_argument('--admin_email', help="Admin email") | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 15 args = parser.parse_args() | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 16 | 
| 
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 17 c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email) | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 18 | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 19 payload = { | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 20 'term': args.term, | 
| 
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 21 } | 
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71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
 iuc parents: diff
changeset | 22 results = c.gquery(**payload) | 
| 1 
0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
 iuc parents: 
0diff
changeset | 23 print(results) | 
