diff --git a/src/find_interaction_cluster/__main__.py b/src/find_interaction_cluster/__main__.py index a196eeb31470ce2123f2453de26b7501059d011b..797bfd86bdf00137ba7cb3b1772402e29d98d028 100644 --- a/src/find_interaction_cluster/__main__.py +++ b/src/find_interaction_cluster/__main__.py @@ -19,13 +19,17 @@ import logging from ..logging_conf import logging_def -@lp.parse +@lp.parse(weight=range(1, 11), global_weight=range(11), + feature=('gene', 'exon'), region=('', 'exon', 'intron', 'gene'), + iteration="iteration > 20", test_type=('lmm', 'perm'), + component_type=("nt", "aa", "dnt")) def launcher(weight: int = 1, global_weight: int = 0, same_gene: bool = True, ps: int = ConfigGraph.cpu, html_fig: bool = False, feature: str = 'exon', region: str = '', - iteration_ppi: int = 1000, + component_type: str = 'nt', + iteration: int = 1000, test_type: str = "lmm", project: str = "GSM1018963_GSM1018964", logging_level: str = "DISABLE"): """ @@ -43,10 +47,14 @@ def launcher(weight: int = 1, :param feature: The feature we want to analyse (default 'exon') :param region: The region of a gene to analyse (used only if feature \ is 'gene') (default '') (can be 'gene', 'exon', 'intron'). + :param component_type: The type of component to analyse; It \ + can be 'nt', 'dnt' or 'aa' (default 'nt'). :param logging_level: The level of data to display (default 'DISABLE') - :param iteration_ppi: the number of iteration for ppi analysis + :param iteration: the number of iteration for ppi and frequency analysis :param project: The project name of interest \ (only used is global_weight = 0). + :param test_type: The king of test to perform for frequency analysis. \ + (default 'lmm') (choose from 'lmm', 'perm') :param ps: The number of processes to use """ logging_def(ConfigGraph.community_folder, __file__, logging_level) @@ -61,10 +69,11 @@ def launcher(weight: int = 1, multiple_stat_launcher(ps, weight, global_weight, project, same_gene, feature, logging_level) multiple_nt_lmm_launcher(ps, weight, global_weight, project, - same_gene, feature, region, logging_level) + same_gene, feature, region, component_type, + test_type, iteration, logging_level) if feature == "gene": ppi_stat_launcher(weight, global_weight, project, same_gene, - ConfigGraph.ppi_threshold, iteration_ppi, + ConfigGraph.ppi_threshold, iteration, logging_level)