From e1c5cc1633d6aa88bc8f2412cf897e8119097511 Mon Sep 17 00:00:00 2001 From: Ravi Bandaru <80599578+ravibandaru-lab@users.noreply.github.com> Date: Thu, 8 Aug 2024 14:16:04 -0500 Subject: [PATCH 1/2] Update main_cli.py --- src/finaletoolkit/cli/main_cli.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/finaletoolkit/cli/main_cli.py b/src/finaletoolkit/cli/main_cli.py index 846e24d..0f78a84 100644 --- a/src/finaletoolkit/cli/main_cli.py +++ b/src/finaletoolkit/cli/main_cli.py @@ -65,6 +65,7 @@ def main_cli_parser(): cli_cleavage_profile = subparsers.add_parser('cleavage-profile', prog='finaletoolkit-cleavage-profile', description='Calculates cleavage proportion over intervals defined in a BED file based on alignment data from a BAM/SAM/CRAM/Fragment file.') cli_cleavage_profile.add_argument('input_file', help='Path to a BAM/SAM/CRAM/Fragment file containing fragment data.') cli_cleavage_profile.add_argument('interval_file', help='Path to a BED file containing intervals to calculates cleavage proportion over.') + cli_adjust_wps.add_argument('genome_file', help='A .chrom.sizes file containing chromosome sizes.') cli_cleavage_profile.add_argument('-o', '--output_file', default='-', help='A bigWig file containing the cleavage proportion results over the intervals specified in interval file.',) cli_cleavage_profile.add_argument('-lo', '--fraction_low', default=120, type=int, help="Minimum length for a fragment to be included in cleavage proportion calculation.") cli_cleavage_profile.add_argument('-hi', '--fraction_high', default=180, type=int, help="Maximum length for a fragment to be included in cleavage proportion calculation.") From 63b9d7ed877fede4109b1f58f2660056082403cb Mon Sep 17 00:00:00 2001 From: Ravi Bandaru <80599578+ravibandaru-lab@users.noreply.github.com> Date: Thu, 8 Aug 2024 14:22:02 -0500 Subject: [PATCH 2/2] Update main_cli.py --- src/finaletoolkit/cli/main_cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/finaletoolkit/cli/main_cli.py b/src/finaletoolkit/cli/main_cli.py index 0f78a84..d765ad0 100644 --- a/src/finaletoolkit/cli/main_cli.py +++ b/src/finaletoolkit/cli/main_cli.py @@ -65,7 +65,7 @@ def main_cli_parser(): cli_cleavage_profile = subparsers.add_parser('cleavage-profile', prog='finaletoolkit-cleavage-profile', description='Calculates cleavage proportion over intervals defined in a BED file based on alignment data from a BAM/SAM/CRAM/Fragment file.') cli_cleavage_profile.add_argument('input_file', help='Path to a BAM/SAM/CRAM/Fragment file containing fragment data.') cli_cleavage_profile.add_argument('interval_file', help='Path to a BED file containing intervals to calculates cleavage proportion over.') - cli_adjust_wps.add_argument('genome_file', help='A .chrom.sizes file containing chromosome sizes.') + cli_cleavage_profile.add_argument('chrom_sizes', help='A .chrom.sizes file containing chromosome sizes.') cli_cleavage_profile.add_argument('-o', '--output_file', default='-', help='A bigWig file containing the cleavage proportion results over the intervals specified in interval file.',) cli_cleavage_profile.add_argument('-lo', '--fraction_low', default=120, type=int, help="Minimum length for a fragment to be included in cleavage proportion calculation.") cli_cleavage_profile.add_argument('-hi', '--fraction_high', default=180, type=int, help="Maximum length for a fragment to be included in cleavage proportion calculation.")