src/find_interaction_cluster/__main__.py: modifications to use the adapt functions

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