Write "no match found" for results list when query had no matches.

scripts/convert_hmmer.py

@@ -9,6 +9,11 @@ parser.add_argument('--output', '-o', required=True, help='The converted results
 parser.add_argument('--dbxref', '-d', required=True, help='The dbxref prefix that will be prepended to the accession or id')
 args = parser.parse_args()
 
+query_file = args.result + "/queries.json"
+queries = []
+with open(query_file) as f:
+    queries = json.load(f)
+
 filename = args.result + "/domtblout.tsv"
 documents = {}
 tool = {'name': None, 'version': None, 'database': None}
@@ -30,7 +35,11 @@ with open(filename) as f:
             query_id = split[3]
             if not query_id in documents:
                 documents[query_id] = {"id": query_id, "computations": [{'tool': tool, 'results':[]}]}
-            results =  documents[query_id]['computations'][0]["results"]
+                try:
+                    queries.remove(query_id)
+                except ValueError:
+                    print('HMMER converter: Query ID "' + query_id + '" not present among initial queries!')
+            results = documents[query_id]['computations'][0]["results"]
 
             results.append({
                 'target': {
@@ -48,6 +57,13 @@ with open(filename) as f:
                     }
                 })
 
+# Include queries with no matches in results
+for query_id in queries:
+    print("In list: " + query_id)
+    if not query_id in documents:
+        print("Recording: " + query_id)
+        documents[query_id] = {"id": query_id, "computations": [{'tool': tool, 'results':"no match found"}]}
+
 output_filename = args.output
 with open(output_filename, 'w') as o:
     json.dump(documents, o)