From 5a8fcdd4d9312f6f8eb41512fc9fdababaeae6e2 Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Thu, 28 Mar 2024 11:28:44 -0400 Subject: [PATCH] :pencil: incorporated some of the PR suggestions --- scripts/cnv_3_gistic_style.py | 2 -- scripts/maf_merge.py | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/scripts/cnv_3_gistic_style.py b/scripts/cnv_3_gistic_style.py index 01d9523..bff8ed5 100755 --- a/scripts/cnv_3_gistic_style.py +++ b/scripts/cnv_3_gistic_style.py @@ -112,8 +112,6 @@ def mt_adjust_cn(obj): data = pd.read_csv(fname, sep="\t") except Exception as e: print(e, file=sys.stderr) - pdb.set_trace() - hold=1 data.set_index("Hugo_Symbol") # sample list would be cbio ids samp_list = list(data.columns)[1:] diff --git a/scripts/maf_merge.py b/scripts/maf_merge.py index b245c1e..bf3b089 100755 --- a/scripts/maf_merge.py +++ b/scripts/maf_merge.py @@ -108,7 +108,7 @@ def process_tbl(cbio_dx, file_meta_dict, print_head): "-i", "--header", action="store", dest="header", help="File with maf header only" ) parser.add_argument( - "-m", "--maf-dirs", action="store", dest="maf_dirs", help="csv of maf file directories" + "-m", "--maf-dirs", action="store", dest="maf_dirs", help="comma-separated list of maf file directories" ) parser.add_argument( "-j",