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1 __author__ = 'cbarnett'
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2 __license__ = "MIT"
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1
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3 __version = "0.3.1"
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4 # http://www.kegg.jp/kegg/rest/keggapi.html
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5
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6
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7 def linked_entries_from_kegg(targetdb="glycan", sourcedb="pathway"):
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8 """
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9 :param targetdb:
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10 :param sourcedb:
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11 :return: string of linked entries
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12 """
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13 import urllib2
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14
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15 uri = 'http://rest.kegg.jp/link/'
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1
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16
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17 import re
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18 p = re.compile(' *\+ *') # ensure no unneccessary space in an AND query
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19 sdbfix = p.subn('+', sourcedb)
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20 sourcedb=sdbfix[0]
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21
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22 if ' ' in sourcedb:
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23 sourcedb = sourcedb.replace(' ', '%20') # previous behaviour was ignoring text after a space, rather convert to '%20' and pass on to KEGG REST service
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24
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25 fulluri = uri + targetdb + "/" + sourcedb
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26 try:
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27 response = urllib2.urlopen(fulluri).read()
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28 except Exception as e:
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29 raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp)
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30 if str(response.strip()) == "":
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31 return ""
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32 return response
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33
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34
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35 if __name__ == "__main__":
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36 from optparse import OptionParser
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37
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38 usage = "usage: python %prog [options]\n"
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39 parser = OptionParser(usage=usage)
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40 parser.add_option("-t", action="store", type="string", dest="t", default="glycan",
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41 help="target db name pathway | brite | module | ko | genome | <org> | compound | glycan | reaction | rpair | rclass | enzyme | disease | drug | dgroup | environ")
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42 parser.add_option("-s", action="store", type="string", dest="s", default="pathway",
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43 help="source db name or db entry e.g. map00010")
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44 parser.add_option("-o", action="store", type="string", dest="o", default="linked_entries.txt",
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45 help="linked entries output in text format")
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46 (options, args) = parser.parse_args()
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47 try:
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48 outstream = file(options.o, 'w')
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49 except Exception as e:
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50 raise IOError(e, "the output file cannot be opened. Use -h flag for help")
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51 linked = linked_entries_from_kegg(targetdb=options.t, sourcedb=options.s)
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52 try:
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53 outstream.write(linked)
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54 except Exception as e:
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55 raise IOError(e, "cannot open output files. -h flag for help")
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56 finally:
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57 outstream.close()
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58
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59
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