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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:29:28 -0500
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28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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()
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 parser.add_option('-g', '--gene-name-col', dest='gene_name_col', help='column of gene names')
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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')
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 parser.add_option('-e', '--expert-curated', dest='expert_curated', action='store_true', help='use only expert curated results')
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 (options, args) = parser.parse_args()
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 gene_name_col = int(options.gene_name_col) - 1
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15
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16 # Open input stream.
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17 if len(args) > 0:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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 # -- Set up gene list queries. --
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23
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24 # Get gene list.
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25 gene_list = []
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 lines = []
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27 for line in input_file:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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)
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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 # Set up gene lists to be ~8K because this is near the max HTTP request length.
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35 gene_list = ','.join(set(gene_list))
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36 queries = []
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37 MAX_QUERY_SIZE = 8000
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38 if len(gene_list) > MAX_QUERY_SIZE:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 # Break queries.
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40 queries = [ gene_list[i:i + MAX_QUERY_SIZE] for i in range(0, len(gene_list), MAX_QUERY_SIZE) ]
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41
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42 # Adjust queries to include whole genes.
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43 for i, query in enumerate( queries[1:] ):
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 part_gene, comma, remainder = query.partition(',')
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45 queries[i] += part_gene
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 queries[i+1] = remainder
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47 else:
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48 queries = [ gene_list ]
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49
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50 # -- Query and process results. --
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51
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52 # Query for results.
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53 results = []
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54 for genes in queries:
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55 query_str = 'http://dgidb.genome.wustl.edu/api/v1/interactions.json?genes=%s' % genes
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56 if options.expert_curated:
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57 query_str += '&source_trust_levels=Expert%20curated'
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58 raw_results = urllib2.urlopen(query_str).read()
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59 results_dict = json.loads(raw_results)
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60 results.extend(results_dict['matchedTerms'])
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61
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62 # Process results.
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63 for result in results:
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64 # Process result.
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65 processed_results = []
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66 result_fields = [ result['geneName'], result['geneLongName'], ','.join( result['geneCategories'] ) ]
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67 for interaction in result['interactions']:
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68 result_fields = result_fields[0:3]
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69 result_fields.extend( [
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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70 interaction['interactionType'], interaction['drugName'], interaction['source']
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71 ] )
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72 processed_results.append( '\t'.join( result_fields ) )
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73
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74 # Store processed results.
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75 results_dict[ result['searchTerm'] ] = processed_results
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76
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77 # -- Annotate input file and produce output. --
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78 for line in lines:
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79 fields = line.split('\t')
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80 gene = fields[gene_name_col]
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81 if gene in results_dict:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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82 for result in results_dict[gene]:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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83 print line.strip() + '\t' + result
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
84 elif options.print_all:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
85 print line
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
86
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
87 if __name__=="__main__": __main__()