Commit ab4892f2 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

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

parent 95dd1a8d
......@@ -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'
format += ' sseqid'
format += ' pident qstart qend sstart send evalue bitscore'
if args.alignment:
format += ' btop'
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