From 2c318eb81ec0fcf095fc5ef2a0f7100303aa78e5 Mon Sep 17 00:00:00 2001 From: Andrey Prjibelski Date: Wed, 17 Apr 2024 18:33:06 +0300 Subject: [PATCH] minor fixes in quantification assessment --- misc/quantification_stats.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/misc/quantification_stats.py b/misc/quantification_stats.py index 4434c528..79f038e4 100755 --- a/misc/quantification_stats.py +++ b/misc/quantification_stats.py @@ -118,7 +118,7 @@ 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() @@ -126,13 +126,11 @@ def 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