Repository 'dgidb_annotator'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator

Changeset 0:8c6dc9da6c89 (2013-11-27)
Next changeset 1:8cc7cf4bd833 (2014-02-25)
Commit message:
Uploaded
added:
dgidb_annotator.py
dgidb_annotator.xml
test-data/in1.tabular
test-data/out1.tabular
b
diff -r 000000000000 -r 8c6dc9da6c89 dgidb_annotator.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dgidb_annotator.py Wed Nov 27 23:51:48 2013 -0500
[
@@ -0,0 +1,64 @@
+'''
+Annotates a tabular file with information from the Drug-Gene Interaction (DGI) database.
+'''
+
+import optparse, json, urllib2, sys
+
+def __main__():
+    # -- Parse command line. --
+    parser = optparse.OptionParser()
+    parser.add_option('-g', '--gene-name-col', dest='gene_name_col', help='column of gene names')
+    parser.add_option('-a', '--print-all', dest='print_all', action='store_true', help='print all lines, even though without a result')
+    parser.add_option('-e', '--expert-curated', dest='expert_curated', action='store_true', help='use only expert curated results')
+    (options, args) = parser.parse_args()
+    gene_name_col = int(options.gene_name_col) - 1
+
+    # Open input stream.
+    if len(args) > 0:
+        input_file = open(args[0], 'r')
+    else:
+        input_file = sys.stdin
+
+    # -- Make connection and get results. --
+
+    # Get gene list.
+    gene_list = []
+    lines = []
+    for line in input_file:
+        gene_list.append( line.split('\t')[gene_name_col].strip() )
+        lines.append(line.strip())
+    
+    # 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)
+    
+    # Process results.
+    matched_results = results_dict['matchedTerms']
+    for result in matched_results:
+        # Process result.
+        processed_results = []
+        result_fields = [ result['geneName'], result['geneLongName'], ','.join( result['geneCategories'] ) ]
+        for interaction in result['interactions']:
+            result_fields = result_fields[0:3]
+            result_fields.extend( [
+                interaction['interactionType'], interaction['drugName'], interaction['source']
+            ] )
+            processed_results.append( '\t'.join( result_fields ) )
+            
+        # Store processed results.
+        results_dict[ result['searchTerm'] ] = processed_results
+
+    # -- Annotate input file and produce output. --
+    for line in lines:
+        fields = line.split('\t')
+        gene = fields[gene_name_col]
+        if gene in results_dict:
+            for result in results_dict[gene]:
+                print line.strip() + '\t' + result
+        elif options.print_all:
+            print line
+
+if __name__=="__main__": __main__()
\ No newline at end of file
b
diff -r 000000000000 -r 8c6dc9da6c89 dgidb_annotator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dgidb_annotator.xml Wed Nov 27 23:51:48 2013 -0500
b
@@ -0,0 +1,45 @@
+<tool id="dgidb_annotator" name="Annotate with DGI" version="0.1">
+    <description>database info</description>
+    
+    <command interpreter="python">
+        dgidb_annotator.py
+        #if $expert_curated_only:
+            -e
+        #end if
+        #if $print_all:
+            -a
+        #end if
+        -g $gene_name_col
+        $input &gt; $output
+    </command>
+    <inputs>
+        <param name="input" label="Input" type="data" format="tabular"/>
+        <param name="expert_curated_only" label="Use Only Expert Curated Results" type="boolean"/>
+        <param name="print_all" label="Print All Rows, including those without Annotation" type="boolean"/>
+        <param name="gene_name_col" label="Gene Name Column" type="data_column" data_ref="input"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+
+    <stdio>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+
+    <tests>
+        <test>
+            <param name="input" value="in1.tabular"/>
+            <param name="expert_curated_only" value="True"/>
+            <param name="print_all" value="False"/>
+            <param name="gene_name_col" value="1"/>
+            <output name="output" file="out1.tabular"/>
+        </test>
+    </tests>
+
+    <help>
+Annotates a tabular dataset with information from the `Drug-Gene Interations database`__
+
+.. __: http://dgidb.genome.wustl.edu/
+    </help>
+</tool>
b
diff -r 000000000000 -r 8c6dc9da6c89 test-data/in1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in1.tabular Wed Nov 27 23:51:48 2013 -0500
b
@@ -0,0 +1,4 @@
+RET gene1
+BIRC3 gene2
+ATM gene3
+KRAS gene4
b
diff -r 000000000000 -r 8c6dc9da6c89 test-data/out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out1.tabular Wed Nov 27 23:51:48 2013 -0500
b
@@ -0,0 +1,44 @@
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE n/a SUNITINIB TEND
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE n/a IMATINIB TEND
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor MOTESANIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor VANDETANIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor SORAFENIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor REGORAFENIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor AMUVATINIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor SUNITINIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor CABOZANTINIB MyCancerGenome
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor SUNITINIB TALC
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor VANDETANIB TALC
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor MOTESANIB TALC
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor CABOZANTINIB TALC
+RET gene1 RET ret proto-oncogene TYROSINE KINASE,DRUGGABLE GENOME,KINASE,CLINICALLY ACTIONABLE inhibitor REGORAFENIB TALC
+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
+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
+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