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1 '''
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2 Annotates a tabular file with information from the Drug-Gene Interaction (DGI) database.
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3 '''
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4
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5 import optparse, json, urllib2, sys, re
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6
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7 def __main__():
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8 # -- Parse command line. --
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9 parser = optparse.OptionParser()
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10 parser.add_option('-g', '--gene-name-col', dest='gene_name_col', help='column of gene names')
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11 parser.add_option('-a', '--print-all', dest='print_all', action='store_true', help='print all lines, even though without a result')
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12 parser.add_option('-e', '--expert-curated', dest='expert_curated', action='store_true', help='use only expert curated results')
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13 (options, args) = parser.parse_args()
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14 gene_name_col = int(options.gene_name_col) - 1
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15
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16 # Open input stream.
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17 if len(args) > 0:
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18 input_file = open(args[0], 'r')
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19 else:
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20 input_file = sys.stdin
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21
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22 # -- Make connection and get results. --
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23
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24 # Get gene list.
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25 gene_list = []
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26 lines = []
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27 for line in input_file:
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28 entry = line.split('\t')[gene_name_col].strip()
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29 # Some annotations may be of the form
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30 # <gene_name>(<splicing_info>) or <gene_name>;<gene_name>(splicing_info)
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31 gene_list.append(entry.split(';')[0].split('(')[0])
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32 lines.append(line.strip())
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33
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34 # Query for results.
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35 query_str = 'http://dgidb.genome.wustl.edu/api/v1/interactions.json?genes=%s' % ','.join(set(gene_list))
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36 if options.expert_curated:
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37 query_str += '&source_trust_levels=Expert%20curated'
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38 print query_str
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39 results = urllib2.urlopen(query_str).read()
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40 results_dict = json.loads(results)
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41
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42 # Process results.
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43 matched_results = results_dict['matchedTerms']
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44 for result in matched_results:
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45 # Process result.
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46 processed_results = []
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47 result_fields = [ result['geneName'], result['geneLongName'], ','.join( result['geneCategories'] ) ]
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48 for interaction in result['interactions']:
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49 result_fields = result_fields[0:3]
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50 result_fields.extend( [
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51 interaction['interactionType'], interaction['drugName'], interaction['source']
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52 ] )
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53 processed_results.append( '\t'.join( result_fields ) )
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54
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55 # Store processed results.
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56 results_dict[ result['searchTerm'] ] = processed_results
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57
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58 # -- Annotate input file and produce output. --
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59 for line in lines:
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60 fields = line.split('\t')
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61 gene = fields[gene_name_col]
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62 if gene in results_dict:
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63 for result in results_dict[gene]:
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64 print line.strip() + '\t' + result
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65 elif options.print_all:
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66 print line
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67
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68 if __name__=="__main__": __main__()
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