src/find_interaction_cluster/__main__.py...

src/find_interaction_cluster/__main__.py src/find_interaction_cluster/community_finder.py: add the parameter use weight

src/find_interaction_cluster/__main__.py

@@ -28,6 +28,7 @@ def launcher(weight: int = 1,
              global_weight: int = 0,
              same_gene: bool = True,
              inflation: float = 1.5,
+             use_weight: bool = False,
              ps: int = ConfigGraph.cpu,
              html_fig: bool = False, feature: str = 'exon', region: str = '',
              component_type: str = 'nt',
@@ -47,6 +48,7 @@ def launcher(weight: int = 1,
     :param same_gene: Say if we consider as co-localised, exons within the \
     same gene (True) or not (False) (default True)
     :param inflation: The inflation parameter
+    :param use_weight: Say if we want to write the weight into the result file.
     :param  html_fig: True to display the html figure (default False).
     :param feature: The feature we want to analyse (default 'exon')
     :param region: The region of a gene to analyse (used only if feature \
@@ -70,21 +72,23 @@ def launcher(weight: int = 1,
         same_gene = True
     if not ConfigGraph.get_hipmcl_prog().is_file():
         install_hipmcl("INFO")
+
     multiple_community_launcher(weight, global_weight, project, same_gene,
-                                inflation, html_fig, feature, logging_level)
+                                inflation, use_weight,
+                                html_fig, feature, logging_level)
     # multiple_stat_launcher(ps, weight, global_weight, project, same_gene,
     #                        inflation, feature, logging_level)
     multiple_nt_lm_launcher(ps, weight, global_weight, project,
                             same_gene, inflation, feature, region,
                             component_type, test_type, iteration, display_size,
                             logging_level=logging_level)
-    if feature == "gene":
-        # ppi_stat_launcher(weight, global_weight, project, same_gene,
-        #                   inflation,
-        #                   ConfigGraph.ppi_threshold, iteration,
-        #                   logging_level)
-        coloc_ppi_stat_main(weight, global_weight, project, same_gene,
-                            inflation, iteration, logging_level)
+    # if feature == "gene":
+    #     # ppi_stat_launcher(weight, global_weight, project, same_gene,
+    #     #                   inflation,
+    #     #                   ConfigGraph.ppi_threshold, iteration,
+    #     #                   logging_level)
+    #     coloc_ppi_stat_main(weight, global_weight, project, same_gene,
+    #                         inflation, iteration, logging_level)
 
 
 

src/find_interaction_cluster/community_finder.py

@@ -313,6 +313,7 @@ def write_interaction_file(arr_interaction: np.array, project: str,
 def community_finder(weight: int, global_weight: int, project: str = "",
                      same_gene=True, html_fig: bool = False,
                      feature: str = "exon", inflation: float = 1.5,
+                     use_weight: bool = True,
                      logging_level: str = "DISABLE"):
     """
     Find communities inside co-localisation between exons found in \
@@ -329,6 +330,7 @@ def community_finder(weight: int, global_weight: int, project: str = "",
     :param logging_level: The level of data to display (default 'DISABLE')
     :param html_fig: True to create an html figure, false else
     :param inflation: The inflation parameter
+    :param use_weight: Say if we want to write the weight into the result file
     :param feature: The feature we want to analyse (default 'exon')
     """
     ConfigGraph.output_folder.mkdir(exist_ok=True, parents=True)
@@ -340,7 +342,8 @@ def community_finder(weight: int, global_weight: int, project: str = "",
     outfile, result_file = write_interaction_file(interaction, project,
                                                   weight, global_weight,
                                                   same_gene, feature=feature,
-                                                  inflation=inflation)
+                                                  inflation=inflation,
+                                                  use_weight=use_weight)
     graph = create_graph(interaction)
     df, dic_community = find_communities(graph, project, outfile, result_file,
                                          feature, inflation)
@@ -380,6 +383,7 @@ def multiple_community_launcher(weight: int,
                                 project: str,
                                 same_gene: bool,
                                 inflation: float = 1.5,
+                                use_weight: bool = False,
                                 html_fig: bool = False,
                                 feature: str = 'exon',
                                 logging_level: str = "DISABLE"):
@@ -391,6 +395,7 @@ def multiple_community_launcher(weight: int,
     :param same_gene: Say if we consider as co-localised exon within the \
     same gene
     :param inflation: The inflation parameter
+    :param use_weight: Say if we want to write the weight into the result file
     :param html_fig: True to create an html figure, false else
     :param feature: The feature we want to analyse (default 'exon')
     :param project: The project name, used only if global_weight = 0
@@ -402,4 +407,4 @@ def multiple_community_launcher(weight: int,
     logging.info(f'Finding community for project : {project}, '
                  f'global_weight : {global_weight}, weight: {weight}')
     community_finder(weight, global_weight, project, same_gene, html_fig,
-                     feature, inflation)
+                     feature, inflation, use_weight)