diff --git a/src/find_interaction_cluster/__main__.py b/src/find_interaction_cluster/__main__.py index 797bfd86bdf00137ba7cb3b1772402e29d98d028..37102fa6918cacba2c6e068d85b068acc3e4c4c9 100644 --- a/src/find_interaction_cluster/__main__.py +++ b/src/find_interaction_cluster/__main__.py @@ -13,15 +13,16 @@ from .config import ConfigGraph from typing import List from .install_hipMCL import install_hipmcl from .sf_and_communities import multiple_stat_launcher -from .nt_and_community import multiple_nt_lmm_launcher +from .nt_and_community import multiple_nt_lm_launcher from .create_ppi_files import ppi_stat_launcher import logging from ..logging_conf import logging_def +from .colocalisation_n_ppi_analysis import coloc_ppi_stat_main @lp.parse(weight=range(1, 11), global_weight=range(11), feature=('gene', 'exon'), region=('', 'exon', 'intron', 'gene'), - iteration="iteration > 20", test_type=('lmm', 'perm'), + iteration="iteration > 20", test_type=('lm', 'perm'), component_type=("nt", "aa", "dnt")) def launcher(weight: int = 1, global_weight: int = 0, @@ -29,7 +30,7 @@ def launcher(weight: int = 1, ps: int = ConfigGraph.cpu, html_fig: bool = False, feature: str = 'exon', region: str = '', component_type: str = 'nt', - iteration: int = 1000, test_type: str = "lmm", + iteration: int = 1000, test_type: str = "lm", project: str = "GSM1018963_GSM1018964", logging_level: str = "DISABLE"): """ @@ -68,13 +69,16 @@ def launcher(weight: int = 1, html_fig, feature, logging_level) 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, component_type, - test_type, iteration, logging_level) + multiple_nt_lm_launcher(ps, weight, global_weight, project, + 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, - logging_level) + # ppi_stat_launcher(weight, global_weight, project, same_gene, + # ConfigGraph.ppi_threshold, iteration, + # logging_level) + coloc_ppi_stat_main(weight, global_weight, project, same_gene, + iteration, logging_level) + launcher() \ No newline at end of file