minor fixes in quantification assessment

misc/quantification_stats.py

@@ -118,21 +118,19 @@ def parse_args():
  parser.add_argument('--tpm', '-t', type=str, help='output expression table to assess, TPM', required=True)
  parser.add_argument('--tpm_col', type=int, default=2, help='TPM column in output expression table')
  parser.add_argument('--tracking', type=str, help='tracking file')
- parser.add_argument('--no_novel', action='store_false', default=True, help='do not use novel transcripts')
+ parser.add_argument('--no_novel', dest="novel", action='store_false', default=True, help='do not use novel transcripts')
  parser.add_argument('--full_stats', action='store_true', default=False, help='output full stats')
  parser.add_argument('--output', '-o', type=str, help='output file', default="quantification_assessment.tsv")
  return parser.parse_args()
 
 
 def main():
  args = parse_args()
- if not os.path.exists(args.output):
- os.makedirs(args.output)
 
  print("Loading reference data from %s" % args.ref_expr)
  ref_tpm_dict = load_counts(args.ref_expr, args.ref_col)
 
- tpm_dict = load_counts(args.tpm, args.tpm_col, novel=not args.no_novel)
+ tpm_dict = load_counts(args.tpm, args.tpm_col, novel=args.no_novel)
 
  if args.tracking:
  # take reference ids from gffcompare output .tracking