diff --git a/src/nt_composition/__main__.py b/src/nt_composition/__main__.py index 9b0bd1187bf4a50fead22fe6f52938920a4ca6f7..a6c34da30296ed4966389ce8e2fb1e93c39f4a9a 100644 --- a/src/nt_composition/__main__.py +++ b/src/nt_composition/__main__.py @@ -21,7 +21,8 @@ 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, inter_chr: bool = False, + community_size: int = -1, inflation: float = 1.5, + inter_chr: bool = False, level: str = "exon", logging_level: str = "DISABLE"): """ @@ -47,6 +48,8 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt', 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 inflation: The inflation parameter. This parameter is used only \ + if community size is not -1. (default 1.5). :param inter_chr: True to only get inter-chromosomal interactions \ False else (default: False) :param level: The kind of feature to analyse (exon or gene) @@ -57,9 +60,9 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt', community_size = None if kind == "density": create_all_frequency_figures(ConfigNt.cpu, weight, global_weight, - ft_type, same_gene, compute_mean, - community_size, inter_chr, level, - logging_level) + ft_type, same_gene, inflation, + compute_mean, community_size, inter_chr, + level, logging_level) else: create_all_distance_figures(ConfigNt.cpu, weight, global_weight, ft_type, same_gene, iteration, inter_chr,