Add configuration whether the id or the accession should be used to blastp runner

bin/run_blastp.py

@@ -11,9 +11,16 @@ parser.add_argument('--database', '-d', required=True, help='Database to search
 parser.add_argument('--output', '-o', required=True, help='The result file')
 parser.add_argument('--evalue', '-e', default='0.0001', help='Evalue cutoff')
 parser.add_argument('--alignment', '-a', action='store_true', help='Include alignments in btop format')
+parser.add_argument('--use_accession', '-x', action='store_true', help='Output the subject accession instead of the whole subject id')
 args = parser.parse_args()
 
-format = '7 qseqid sseqid pident qstart qend sstart send evalue bitscore'
+format = '7 qseqid'
+if args.use_accession:
+    format += ' saccver'
+else:
+    format += ' sseqid'
+format += ' pident qstart qend sstart send evalue bitscore'
+
 if args.alignment:
     format += ' btop'