Merge branch 'fix-include-sequence' into 'develop'

Fix loss of last fasta entry. Solves #31

See merge request SOaAS/psot!7

scripts/convert_fasta.py

 #!/usr/bin/python3
-import sys
+
 import json
 import argparse
 
 parser = argparse.ArgumentParser(description='Convert a fasta file into a json document')
-parser.add_argument('--result', '-r', required=True, help='The fasta file result directory')
+parser.add_argument('--result', '-r', required=True, help='The fasta file')
 parser.add_argument('--output', '-o', required=True, help='The json file')
 args = parser.parse_args()
 
 documents = {}
 with open(args.result) as f:
-    # second scan for data
-    entry = None
+    id = None
     for line in f:
         if line.startswith(">"):
-            id =  line.split()[0][1:]
-            if entry is not None:
-                documents[entry['id']] = entry
-            entry = {'id': id, 'sequence': ''}
-            
-        else:
-            entry['sequence'] = entry['sequence'] + line.strip()
+            id = line.split()[0][1:]
+            documents[id] = {'id': id, 'sequence': ''}
+        elif id is not None:
+            documents[id]['sequence'] += line.strip()
 
 output_filename = args.output
 with open(output_filename, 'w') as o: