diff --git a/tobias/footprinting/scorebigwig.py b/tobias/footprinting/scorebigwig.py index 356970a..4cb6466 100644 --- a/tobias/footprinting/scorebigwig.py +++ b/tobias/footprinting/scorebigwig.py @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -FootprintScores: Calculate footprint tracks from cutsite bigwig +ScoreBigwig: Calculate footprint tracks from cutsite bigwig @author: Mette Bentsen @contact: mette.bentsen (at) mpi-bn.mpg.de @@ -37,7 +37,7 @@ def add_scorebigwig_arguments(parser): description = "ScoreBigwig calculates scores (such as footprint-scores) from bigwig files (such as ATAC-seq cutsites calculated using the ATACorrect tool).\n\n" description += "Usage: ScoreBigwig --signal --regions --output \n\n" description += "Output:\n- " - parser.description = format_help_description("FootprintScores", description) + parser.description = format_help_description("ScoreBigwig", description) parser._action_groups.pop() #pop -h @@ -57,10 +57,10 @@ def add_scorebigwig_arguments(parser): optargs.add_argument('--max-limit', metavar="", type=float, help="Limit input bigwig score range (default: no upper limit)") #default none footprintargs = parser.add_argument_group('Parameters for score == footprint') - optargs.add_argument('--fp-min', metavar="", type=int, help="Minimum footprint width (default: 20)", default=20) - optargs.add_argument('--fp-max', metavar="", type=int, help="Maximum footprint width (default: 50)", default=50) - optargs.add_argument('--flank-min', metavar="", type=int, help="Minimum range of flanking regions (default: 10)", default=10) - optargs.add_argument('--flank-max', metavar="", type=int, help="Maximum range of flanking regions (default: 30)", default=30) + footprintargs.add_argument('--fp-min', metavar="", type=int, help="Minimum footprint width (default: 20)", default=20) + footprintargs.add_argument('--fp-max', metavar="", type=int, help="Maximum footprint width (default: 50)", default=50) + footprintargs.add_argument('--flank-min', metavar="", type=int, help="Minimum range of flanking regions (default: 10)", default=10) + footprintargs.add_argument('--flank-max', metavar="", type=int, help="Maximum range of flanking regions (default: 30)", default=30) sumargs = parser.add_argument_group('Parameters for score == sum') sumargs.add_argument('--window', metavar="", type=int, help="The window for calculation of sum (default: 100)", default=100) @@ -141,7 +141,7 @@ def run_scorebigwig(args): logger = TobiasLogger("ScoreBigwig", args.verbosity) logger.begin() - parser = add_footprint_arguments(argparse.ArgumentParser()) + parser = add_scorebigwig_arguments(argparse.ArgumentParser()) logger.arguments_overview(parser, args) logger.output_files([args.output]) diff --git a/tobias/motifs/tfbscan.py b/tobias/motifs/tfbscan.py index 68d4767..4937d40 100644 --- a/tobias/motifs/tfbscan.py +++ b/tobias/motifs/tfbscan.py @@ -49,7 +49,7 @@ def add_tfbscan_arguments(parser): optional_arguments.add_argument('--gc', metavar="", type=lambda x: restricted_float(x,0,1), help='Set the gc content for background regions (default: will be estimated from fasta)') optional_arguments.add_argument('--pvalue', metavar="", type=lambda x: restricted_float(x,0,1), help='Set p-value for motif matches (default: 0.0001)', default=0.0001) optional_arguments.add_argument('--keep-overlaps', action='store_true', help='Keep overlaps of same motifs (default: overlaps are resolved by keeping best-scoring site)') - optional_arguments.add_argument('--add-region-columns', action='store_true', help="Add extra information columns (from 4th column) from --regions to the output .bed-file(s) (default: off)") + optional_arguments.add_argument('--add-region-columns', action='store_true', help="Add extra information columns (starting from 4th column) from --regions to the output .bed-file(s) (default: off)") RUN = parser.add_argument_group('Run arguments') RUN.add_argument('--split', metavar="", type=int, help="Split of multiprocessing jobs (default: 100)", default=100)