edited cami_suite

cami_src/cami_suite.py

@@ -14,6 +14,15 @@ import itertools
 
 
 def generate_param_combinations(params_dict):
+    """
+    Generates all possible combinations of parameters for the given function(s) and returns them as a list.
+
+    Args:
+        params_dict (dict): A dictionary containing the parameters and their possible values for each function.
+
+    Returns:
+        list: A list of lists where each inner list contains the function name, parameter string, and a dictionary with the parameter values and corresponding function.
+    """
     params_keys = list(params_dict.keys())
     params_values = [params_dict[k] for k in params_keys if k != 'function']
     function_dict = params_dict['function']
@@ -110,6 +119,7 @@ class cami():
         self.seed_lst = seed_lst
         self.origin_seed_lst = seed_lst.copy()
         self.tool_wrappers = tool_wrappers
+        self.prediction_tools = [wrapper.name for wrapper in tool_wrappers]
         self.toolweights = toolweights
         self.home_path = home_path
         if uid==None:
@@ -347,18 +357,24 @@ class cami():
                                  'first_neighbours': cami_v1.make_first_neighbor_result_set}
                     }
         
-        params_tr = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0], 
-                     'damping_factor': [0.1, 0.25, 0.5, 0.75], 
-                     'confidence_level': [0.2, 0.35, 0.5, 0.75],
+        params_tr = {'hub_penalty': [0.5], 
+                     'damping_factor': [0.5], 
+                     'confidence_level': [0.5],
                      'ranking': ['trustrank'],
                      'function': {'cami_v2': cami_v2.run_cami, 
                                   'cami_v3':cami_v3.run_cami}}
         
-        params_b_m = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0], 
-                     'confidence_level': [0.2, 0.35, 0.5, 0.75],
+        params_b_m = {'hub_penalty': [0.5], 
+                     'confidence_level': [0.5],
                      'ranking': ['betweenness', 'harmonic'],
                      'function': {'cami_v2': cami_v2.run_cami,
-                                  'cami_v3':cami_v3.run_cami}}
+                                  'cami_v3':cami_v3.run_cami}}        
+                
+        # params_b_m = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0], 
+        #              'confidence_level': [0.2, 0.35, 0.5, 0.75],
+        #              'ranking': ['betweenness', 'harmonic'],
+        #              'function': {'cami_v2': cami_v2.run_cami,
+        #                           'cami_v3':cami_v3.run_cami}}
         
         c = generate_param_combinations(params_0)
         cami_setting_list = generate_param_combinations(params_0)+\
@@ -369,7 +385,7 @@ class cami():
         camis = {}
         for setting in cami_setting_list:
             if setting[1]:
-                func_name = setting[0] + '_' +setting[1]
+                func_name = setting[0] + '_' +setting[1].rsplit('_', 1)[-1]
             else:
                 func_name = setting[0]
             
@@ -553,7 +569,7 @@ class cami():
         else:
             print('Cannot use degradome to create venn diagrams of 6 or more tools')
             return None
-
+        
     def download_diagram(self, url):
         venn_name = f'{self.output_dir}/vdiagram_{self.uid}'
         response = degradome.download_image(url, venn_name + '.png')