src/find_interaction_cluster/clip_figures/__main__.py: add 3 new parameters:...

src/find_interaction_cluster/clip_figures/__main__.py: add 3 new parameters: display_size, community_file and ps

src/find_interaction_cluster/clip_figures/__main__.py

@@ -13,14 +13,18 @@ from .clip_analyser import clip_folder_analysis
 
 
 @lp.parse(test_type=["permutation", "lm"], feature=["gene", "exon"])
-def clip_analysis(clip_folder: str, weight: int,
-                  global_weight: int, same_gene: bool = True,
+def clip_analysis(clip_folder: str, weight: int = -1,
+                  global_weight: int = -1, same_gene: bool = True,
                   feature: str = "exon",
                   project: str = "GSM1018963_GSM1018964",
                   test_type: str = "permutation", iteration: int = 10000,
+                  display_size: bool=False,
+                  community_file: str = "",
+                  ps: int = 1,
                   logging_level: str = "DEBUG") -> None:
     """
-    Create the final figure
+    Create the final figure.
+
     :param project: The name of the project of interest
     :param weight: The minimum weight of interaction to consider
     :param global_weight: The global weight to consider. if \
@@ -34,9 +38,18 @@ def clip_analysis(clip_folder: str, weight: int,
     :param test_type: The kind of test to perform for frequency analysis. \
     (default 'lm') (choose from 'lm', 'permutation')
     :param iteration: The number of iteration
+    :param display_size: True to display the size of the community. \
+    False to display nothing. (default False)
+    :param community_file: A file containing custom communities. If \
+    it equals to '' then weight, global weight and same genes parameter are \
+    used to find the community files computed with ChIA-PET data.
+    :param ps: The number of processes to create (default 1)
     :param logging_level: The level of data to display (default 'DISABLE')
     :return: The final dataframe that can be used to create clip figures
     """
+    if (weight == -1 or global_weight == -1) and community_file == "":
+        raise ValueError(f"Global weight or weight can't be equal to one if "
+                         f"community_file is not defined !")
     clip_folder = Path(clip_folder)
     if test_type == "lm":
         raise NotImplementedError("test_type for lm is not implemented !")
@@ -44,7 +57,7 @@ def clip_analysis(clip_folder: str, weight: int,
         raise NotADirectoryError(f"{clip_folder} is not an existing directory")
     clip_folder_analysis(clip_folder, project, weight, global_weight,
                          same_gene, feature, test_type, iteration,
-                         logging_level)
+                         display_size, community_file, ps, logging_level)
 
 
 clip_analysis()
\ No newline at end of file