annotate ecitmatch.py @ 2:08412cd072d0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
author iuc
date Wed, 11 Mar 2020 04:02:33 -0400
parents 28f69754ddc5
children d1789b4821fc
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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4 import argparse
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6 import eutils
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9 if __name__ == '__main__':
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10 parser = argparse.ArgumentParser(description='ECitMatch', epilog='')
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11 parser.add_argument('--file', type=argparse.FileType('r'), help='Tabular file containing citations to search')
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13 parser.add_argument('--key', nargs='*', help='Citation Key')
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14 parser.add_argument('--journal_title', nargs='*', help='Journal Title')
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15 parser.add_argument('--year', nargs='*', help='Year')
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16 parser.add_argument('--volume', nargs='*', help='Volume')
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17 parser.add_argument('--first_page', nargs='*', help='First Page')
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18 parser.add_argument('--author_name', nargs='*', help='Author name')
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20 # Emails
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21 parser.add_argument('--user_email', help="User email")
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22 parser.add_argument('--admin_email', help="Admin email")
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23 args = parser.parse_args()
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25 c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email)
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27 citations = []
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28 if args.file is None:
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29 for key, journal, year, volume, first_page, author_name in \
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30 zip(args.key, args.journal_title, args.year, args.volume, args.first_page, args.author_name):
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31 citations.append({
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32 'key': key,
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33 'journal': journal,
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34 'year': year,
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35 'volume': volume,
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36 'first_page': first_page,
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37 'author_name': author_name,
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38 })
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39 else:
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40 for line in args.file:
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41 line = line.strip()
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42 if not line.startswith('#'):
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43 tmp = line.split('\t')
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44 try:
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45 citations.append({
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46 'journal': tmp[0],
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47 'year': tmp[1],
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48 'volume': tmp[2],
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49 'first_page': tmp[3],
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50 'author_name': tmp[4],
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51 'key': tmp[5],
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52 })
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53 except KeyError:
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54 print("Could not parse line: %s" % line)
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56 payload = {
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57 'db': 'pubmed',
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58 'bdata': citations
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59 }
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61 results = c.citmatch(**payload)
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62 # We get data back as pipe separated, so just replace those with tabs
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63 print(results.replace('|', '\t'))