From e8d19aad2d2e0d05c02b4fc1edbcb1d03bd0bc11 Mon Sep 17 00:00:00 2001 From: ashuaibi7 Date: Sun, 12 Jan 2025 12:46:41 -0500 Subject: [PATCH] reorder arguments added to simulate parser to match order of arguments passed into create single gene method --- src/dialect/utils/argument_parser.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/src/dialect/utils/argument_parser.py b/src/dialect/utils/argument_parser.py index 4124478..0f3de1f 100644 --- a/src/dialect/utils/argument_parser.py +++ b/src/dialect/utils/argument_parser.py @@ -107,12 +107,6 @@ def add_simulate_create_single_gene_parser(subparsers): single_gene_parser = subparsers.add_parser( "single", help="Create single gene simulations" ) - single_gene_parser.add_argument("-s", "--seed", type=int, default=42) - single_gene_parser.add_argument("-n", "--num_samples", type=int, default=1000) - single_gene_parser.add_argument("-o", "--out", type=str, required=True) - single_gene_parser.add_argument("-ns", "--num_simulations", type=int, default=2500) - single_gene_parser.add_argument("-b", "--bmr", help="Path to the BMR file") - single_gene_parser.add_argument("-g", "--gene", type=str, help="Gene name") single_gene_parser.add_argument( "-pi", "--pi", @@ -124,6 +118,16 @@ def add_simulate_create_single_gene_parser(subparsers): required=True, help="Pi value (must be between 0 and 1)", ) + single_gene_parser.add_argument("-n", "--num_samples", type=int, default=1000) + single_gene_parser.add_argument("-ns", "--num_simulations", type=int, default=2500) + single_gene_parser.add_argument( + "-b", "--bmr", required=True, help="Path to the BMR file" + ) + single_gene_parser.add_argument( + "-g", "--gene", required=True, type=str, help="Gene name" + ) + single_gene_parser.add_argument("-o", "--out", type=str, required=True) + single_gene_parser.add_argument("-s", "--seed", type=int, default=42) # TODO add support for binomial BMR (exclusive of real bmr) # single_gene_parser.add_argument("-l", "--length", type=int, default=10000)