Implement simple storage of query sequence names. Currently relies on resolution of issue #22.

scripts/run_hmmer.py

 #!/usr/bin/env python3
 import env
 import argparse
+import json
 from psot import config
 from os import system, makedirs
 
@@ -22,3 +23,15 @@ system(hmmscan_tool +
         " --domtblout " + args.output + "/domtblout.tsv " + 
         " --pfamtblout " + args.output + "/pfamtblout.tsv " + 
         args.database + " " +  args.fasta)
+
+# Provide a list of all query sequence names for conversion process
+queries = []
+
+with open(args.fasta) as f:
+    for line in f:
+        if line.startswith('>'):
+            queries.append(line.replace('>', '').strip())
+
+query_file = args.output + '/' + 'queries.json'
+with open(query_file, 'w') as o:
+    json.dump(queries, o)