Minor code cosmetics

scripts/convert_hmmer.py

@@ -38,7 +38,7 @@ with open(filename) as f:
                 try:
                     queries.remove(query_id)
                 except ValueError:
-                    print('HMMER converter: Query ID "' + query_id + '" not present among initial queries!')
+                    print('HMMER converter: Query ID "' + query_id + '" not found among initial queries!')
             results = documents[query_id]['computations'][0]["results"]
 
             results.append({
@@ -57,11 +57,8 @@ 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

scripts/run_hmmer.py

@@ -18,7 +18,7 @@ makedirs(args.output, exist_ok=True)
 
 system(hmmscan_tool + 
         " -E " + args.evalue + 
-        " -o " +args.output+ "/hmmscan.out " + 
+        " -o " + args.output + "/hmmscan.out " + 
         " --tblout " + args.output + "/tblout.tsv "  + 
         " --domtblout " + args.output + "/domtblout.tsv " + 
         " --pfamtblout " + args.output + "/pfamtblout.tsv " + 
@@ -32,6 +32,6 @@ with open(args.fasta) as f:
         if line.startswith('>'):
             queries.append(line.replace('>', '').strip())
 
-query_file = args.output + '/' + 'queries.json'
+query_file = args.output + '/queries.json'
 with open(query_file, 'w') as o:
     json.dump(queries, o)