adapted resolve_dbxrefs.py to input format

scripts/resolve_dbxrefs.py

@@ -7,7 +7,7 @@ import sys
 parser = argparse.ArgumentParser(description='Resolve dbxrefs from json file')
 parser.add_argument('--input', '-i', required=True, help='The json input document')
 parser.add_argument('--retriever', '-s', required=True, help='Location of retriever')
-parser.add_argument('--output', '-o', required=True, help='Name of the output document')
+#parser.add_argument('--output', '-o', required=True, help='Name of the output document')
 args = parser.parse_args()
 
 basename = args.retriever.replace('scripts/', '')
@@ -18,13 +18,16 @@ from retriever import retrieve
 
 json_file = open(args.input).read()
 j = json.loads(json_file)
-di = []
+#di = []
 
 for c in j['computations']:
     for r in c['results']:
-        di = retrieve(r['informations'], basename)
-
-output_filename = args.output
-with open(output_filename, 'w') as o:
-    json.dump(di, o)
+        if 'target'in r and 'dbxref' in r['target']:
+            di = retrieve([r['target']['dbxref']], basename)
+            r['target']['dbxref'] = {'dbxref': r['target']['dbxref'], 'informations': di[0]}
+
+#output_filename = args.output
+#with open(output_filename, 'w') as o:
+with open(args.input, 'w') as o:
+    json.dump(j, o)
 

testfiles/resolver_test.json

@@ -9,21 +9,186 @@
 			},
 			"results" : [
 				{
-					"score" : "42",
-					"alignment" : "|||||||||||||||||||||||||||",
-					"informations" : [
-						"UniProtKB/Swiss-Prot:Q5XI95",
-						"UniProtKB/Swiss-Prot:Q70UN9",
-						"GO:0008270",
-						"GO:0004024",
-						"GO:0004930",
-						"EC:1.1.1.1",
-						"EC:2.2.1.1",
-						"PFAM:PF00002",
-						"PFAM:PF08240",
-						"SO:0000022",
-						"SO:0000714"
-					]
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "UniProtKB/Swiss-Prot:Q5XI95"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "UniProtKB/Swiss-Prot:Q70UN9"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:0008270"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:0004024"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:0004930"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "EC:1.1.1.1"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "EC:2.2.1.1"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "PFAM:PF00002"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "PFAM:PF08240"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "SO:0000022"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "SO:0000714"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:0005737"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:0004022"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:0008270"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "Pfam:PF08240"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "SO:0000380"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "SO:0000026"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "SO:0000020"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "UniProtKB/Swiss-Prot:P09370"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "UniProtKB/Swiss-Prot:P22246"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "UniProtKB/Swiss-Prot:P08843"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "GO:001"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "EC:2.1"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "Pfam:PF040"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "SO:020"
+					}
+				},
+				{
+					"target" : {
+						"score" : "42",
+						"alignment" : "|||||||||||||||||||||||||||",
+						"dbxref" : "UniProtKB/Swiss-Prot:P09"
+					}
 				}
 			]
 		}