From 80219951c0179c9a98f5ea6684a3d510fb95fc0d Mon Sep 17 00:00:00 2001 From: Pedro Mendes Date: Mon, 17 Jun 2024 21:23:43 -0400 Subject: [PATCH] new option for medium volume --- sbmodelr | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/sbmodelr b/sbmodelr index 6b03b08..618cdd5 100755 --- a/sbmodelr +++ b/sbmodelr @@ -284,6 +284,7 @@ parser.add_argument('--pn', dest='noisy', help='add noise to parameter with leve parser.add_argument('--cn', dest='cnoise', help='add noise to all coupling parameters with level magnitude, dist: {uni,norm}', nargs=2, metavar=('level', 'dist')) # other options parser.add_argument('--add-medium', action='store_true', help='add a medium unit with all transported species') +parser.add_argument('--medium-volume', type=positive_float, help='volume of medium unit', default='1.0', metavar='value') parser.add_argument('--ignore-compartments', action='store_true', help='do not replicate compartments') parser.add_argument('--ignore-tasks', action='store_true', help='do not copy over task settings') parser.add_argument('--sbml', choices=['l1v2', 'l2v3', 'l2v4', 'l2v5', 'l3v1', 'l3v2'], help='export in SBML format of this level and version.') @@ -319,6 +320,9 @@ grnV = args.grn_V grna = args.grn_a grnh = args.grn_h +# medium volume +mediumVol = args.medium_volume + # check if level for --cn is a positive float and distribution is allowed if( args.cnoise ): (level, dist) = args.cnoise @@ -1004,7 +1008,7 @@ if( args.add_medium ): if((mcomps is not None) and (medium_name in mcomps.index)): medium_name = '_added_medium_' # create medium compartment - add_compartment(model=newmodel, name=medium_name, status='fixed', initial_size=1, dimiensionality=3, notes="medium compartment added by sbmodlr" ) + add_compartment(model=newmodel, name=medium_name, status='fixed', initial_size=mediumVol, dimiensionality=3, notes="medium compartment added by sbmodlr" ) # create the species that are transported if( transported ): for (sp,ttype) in transported: