diff --git a/src/nt_composition/__main__.py b/src/nt_composition/__main__.py index 3f931ee78885b9fd730d25da4dddb73993b50b96..72e99bbc3c22e8de467f9686b467009d397de89b 100644 --- a/src/nt_composition/__main__.py +++ b/src/nt_composition/__main__.py @@ -21,6 +21,7 @@ import lazyparser as lp def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt', same_gene: bool = False, compute_mean: bool = True, iteration: int = 10000, kind: str = 'density', + community_size: int = -1, logging_level: str = "DISABLE"): """ Launch the creation of density file. @@ -42,13 +43,18 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt', correlation figure between the feature frequency of an exon and the \ frequency of the same feature for other co-localized exons. 'distance' \ to check if the frequencies of co-localized exon are closer than \ - randomly expected. (default : 'density'). + randomly expected. (default : 'density').* + :param community_size: consider only exons within communities bigger + than community size. if community_size = -1. This option is deactivated. :param logging_level: The level of data to display (default 'DISABLE') """ get_interactions_number(weight, same_gene, logging_level) + if community_size == -1: + community_size = None if kind == "density": create_all_frequency_figures(ConfigNt.cpu, weight, global_weight, ft_type, same_gene, compute_mean, + community_size, logging_level) else: create_all_distance_figures(ConfigNt.cpu, weight, global_weight,