Added --result and --output options to json converter scripts

bin/convert_blast_swissprot.py

 #!/usr/bin/python3
 import sys
 import json
+import argparse
 
-filename = sys.argv[1]
+parser = argparse.ArgumentParser(description='Convert blast results to json documents')
+parser.add_argument('--result', '-r', required=True, help='The blast result file in outfmt 7 format (tsv with headers)')
+parser.add_argument('--output', '-o', required=True, help='The converted results json file')
+args = parser.parse_args()
+
+filename = args.result
 documents = {}
 with open(filename) as f:
     header = None
@@ -44,6 +50,6 @@ with open(filename) as f:
 
             results.append(result)
 
-
-for key in documents:
-    print(json.dumps(documents[key]))
+output_filename = args.output
+with open(output_filename, 'w') as o:
+    json.dump(documents, o)

bin/convert_signalp.py

 #!/usr/bin/python3
 import sys
 import json
+import argparse
 
-filename = sys.argv[1]
+parser = argparse.ArgumentParser(description='Convert signalp results to json documents')
+parser.add_argument('--result', '-r', required=True, help='The signalp result file')
+parser.add_argument('--output', '-o', required=True, help='The converted results json file')
+args = parser.parse_args()
+
+filename = args.result
 documents = {}
 with open(filename) as f:
     tool = None
@@ -29,5 +35,6 @@ with open(filename) as f:
                         'version': split[1].split('-')[1],
                         'mode': split[2]}
 
-for key in documents:
-    print(json.dumps(documents[key]))
+output_filename = args.output
+with open(output_filename, 'w') as o:
+    json.dump(documents, o)