From 2c6223cc904b44fcb456112f6a1e89d3249199a7 Mon Sep 17 00:00:00 2001 From: Katharina Hoff Date: Wed, 4 Sep 2019 15:15:07 +0200 Subject: [PATCH] fix_in_frame_stop_codon_genes.py : added command line option --cdbtools_path --- scripts/fix_in_frame_stop_codon_genes.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/scripts/fix_in_frame_stop_codon_genes.py b/scripts/fix_in_frame_stop_codon_genes.py index 18340d16..f43018c6 100755 --- a/scripts/fix_in_frame_stop_codon_genes.py +++ b/scripts/fix_in_frame_stop_codon_genes.py @@ -109,6 +109,9 @@ parser.add_argument('-p', '--print_format_examples', required=False, action='store_true', help="Print gtf/gff3 input format \ examples, do not perform analysis") +parser.add_argument('-C', '--cdbtools_path', required=False, type=str, + help = "Set path to cdbfasta/cdbyank. If not given, \ + will try to locate the path with which(cdbfasta).") args = parser.parse_args() ### As args.hintsfile and args.extrinsicCfgFile have to be given together: ### @@ -298,8 +301,12 @@ def sortSecond(val): ### Find required binaries on system ### grep = find_tool("grep") perl = find_tool("perl") -cdbfasta = find_tool("cdbfasta") -cdbyank = find_tool("cdbyank") +if args.cdbtools_path: + cdbfasta = check_tool_in_given_path(args.cdbtools_path, "cdbfasta") + cdbyank = check_tool_in_given_path(args.cdbtools_path, "cdbyank") +else: + cdbfasta = find_tool("cdbfasta") + cdbyank = find_tool("cdbyank") ### Find augustus_bin_path ### if args.augustus_bin_path: