Mercurial > repos > devteam > dgidb_annotator
changeset 3:c5bb987015c5 draft default tip
Uploaded
| author | devteam |
|---|---|
| date | Fri, 07 Mar 2014 16:34:26 -0500 |
| parents | 792f3cb0eff4 |
| children | |
| files | dgidb_annotator.py dgidb_annotator.xml test-data/out1.tabular |
| diffstat | 3 files changed, 53 insertions(+), 31 deletions(-) [+] |
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--- a/dgidb_annotator.py Tue Feb 25 14:19:17 2014 -0500 +++ b/dgidb_annotator.py Fri Mar 07 16:34:26 2014 -0500 @@ -2,7 +2,7 @@ Annotates a tabular file with information from the Drug-Gene Interaction (DGI) database. ''' -import optparse, json, urllib2, sys, re +import optparse, json, urllib2, sys def __main__(): # -- Parse command line. -- @@ -19,7 +19,7 @@ else: input_file = sys.stdin - # -- Make connection and get results. -- + # -- Set up gene list queries. -- # Get gene list. gene_list = [] @@ -31,16 +31,36 @@ gene_list.append(entry.split(';')[0].split('(')[0]) lines.append(line.strip()) + # Set up gene lists to be ~8K because this is near the max HTTP request length. + gene_list = ','.join(set(gene_list)) + queries = [] + MAX_QUERY_SIZE = 8000 + if len(gene_list) > MAX_QUERY_SIZE: + # Break queries. + queries = [ gene_list[i:i + MAX_QUERY_SIZE] for i in range(0, len(gene_list), MAX_QUERY_SIZE) ] + + # Adjust queries to include whole genes. + for i, query in enumerate( queries[1:] ): + part_gene, comma, remainder = query.partition(',') + queries[i] += part_gene + queries[i+1] = remainder + else: + queries = [ gene_list ] + + # -- Query and process results. -- + # Query for results. - query_str = 'http://dgidb.genome.wustl.edu/api/v1/interactions.json?genes=%s' % ','.join(set(gene_list)) - if options.expert_curated: - query_str += '&source_trust_levels=Expert%20curated' - results = urllib2.urlopen(query_str).read() - results_dict = json.loads(results) - + results = [] + for genes in queries: + query_str = 'http://dgidb.genome.wustl.edu/api/v1/interactions.json?genes=%s' % genes + if options.expert_curated: + query_str += '&source_trust_levels=Expert%20curated' + raw_results = urllib2.urlopen(query_str).read() + results_dict = json.loads(raw_results) + results.extend(results_dict['matchedTerms']) + # Process results. - matched_results = results_dict['matchedTerms'] - for result in matched_results: + for result in results: # Process result. processed_results = [] result_fields = [ result['geneName'], result['geneLongName'], ','.join( result['geneCategories'] ) ]
--- a/dgidb_annotator.xml Tue Feb 25 14:19:17 2014 -0500 +++ b/dgidb_annotator.xml Fri Mar 07 16:34:26 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="dgidb_annotator" name="Annotate with DGI" version="0.1"> +<tool id="dgidb_annotate" name="Annotate with DGI" version="0.1"> <description>database info</description> <command interpreter="python">
--- a/test-data/out1.tabular Tue Feb 25 14:19:17 2014 -0500 +++ b/test-data/out1.tabular Fri Mar 07 16:34:26 2014 -0500 @@ -15,30 +15,32 @@ RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor LENVATINIB TALC RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor AMUVATINIB TALC RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor AT9283 TALC +RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE n/a VANDETANIB ClearityFoundationClinicalTrial +RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE n/a DOVITINIB ClearityFoundationClinicalTrial BIRC3 gene2 BIRC3 baculoviral IAP repeat containing 3 antagonist AEG40826 TALC BIRC3 gene2 BIRC3 baculoviral IAP repeat containing 3 antagonist TL 32711 TALC BIRC3 gene2 BIRC3 baculoviral IAP repeat containing 3 antagonist AT-406 TALC BIRC3 gene2 BIRC3 baculoviral IAP repeat containing 3 antagonist GDC0917 TALC BIRC3 gene2 BIRC3 baculoviral IAP repeat containing 3 antagonist LCL161 TALC -ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a E7449 ClearityFoundation -ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a NIRAPARIB ClearityFoundation -ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a OLAPARIB ClearityFoundation -ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a BMN673 ClearityFoundation -ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a RUCAPARIB ClearityFoundation -ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a VELIPARIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a VANDETANIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a EVEROLIMUS ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a TEMSIROLIMUS ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a GDC-0973 ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a MEK162 ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a PD-325901 ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a RAFAMETINIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a SELUMETINIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a TRAMETINIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a CETUXIMAB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a ERLOTINIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a GEFITINIB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a PANITUMUMAB ClearityFoundation -KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a PIMASERTIB ClearityFoundation +ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a E7449 ClearityFoundationBiomarkers +ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a NIRAPARIB ClearityFoundationBiomarkers +ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a OLAPARIB ClearityFoundationBiomarkers +ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a BMN673 ClearityFoundationBiomarkers +ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a RUCAPARIB ClearityFoundationBiomarkers +ATM gene3 ATM ataxia telangiectasia mutated PHOSPHATIDYLINOSITOL 3 KINASE,DRUGGABLE GENOME,CLINICALLY ACTIONABLE,SERINE THREONINE KINASE,KINASE,TUMOR SUPPRESSOR,DNA REPAIR n/a VELIPARIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a VANDETANIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a EVEROLIMUS ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a TEMSIROLIMUS ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a GDC-0973 ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a MEK162 ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a PD-325901 ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a RAFAMETINIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a SELUMETINIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a TRAMETINIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a CETUXIMAB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a ERLOTINIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a GEFITINIB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a PANITUMUMAB ClearityFoundationBiomarkers +KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE n/a PIMASERTIB ClearityFoundationBiomarkers KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE inhibitor REOLYSIN CancerCommons KRAS gene4 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CLINICALLY ACTIONABLE vaccine RAS PEPTIDE CANCER VACCINE TALC