bugs fixed save_models

xpore/diffmod/gmm.py

@@ -241,6 +241,7 @@ def _update(self, children):
         prob = 1./(1.+np.exp(np.clip(ln_rho_diff, -500, 500)))  # N,1 => N
         self.params['prob'] = np.stack([prob, 1-prob], axis=-1)
         self.params['ln_prob'] = ln_rho - scipy.special.logsumexp(ln_rho, axis=-1)[..., newaxis]  # N,K
+
 
 
 class Dirichlet(object):

xpore/diffmod/io.py

@@ -96,7 +96,7 @@ def save_result_table(table, out_filepath):
     out_file.close()
 
 
-def save_models(models, model_filepath):  # per gene/transcript
+def save_models_to_hdf5(models, model_filepath):  # per gene/transcript
     """
     Save model parameters.
 
@@ -124,7 +124,7 @@ def save_models(models, model_filepath):  # per gene/transcript
         model_file[idx][position].create_group('nodes')  # ['x','y','z','w','mu_tau'] => store only their params
         for node_name in model.nodes:
             model_file[idx][position]['nodes'].create_group(node_name)
-            if model.nodes[node_name].data is not None: # To make it optional.
+            if model.nodes[node_name].data is not None: # Todo: make it optional.
                 value = model.nodes[node_name].data
                 if node_name in ['y_run_names','y_condition_names']:
                     value = [val.encode('UTF-8') for val in value]

xpore/scripts/diffmod.py

@@ -80,7 +80,8 @@ def execute(idx, data_dict, data_info, method, criteria, model_kmer, prior_param
 
     if save_models & (len(models)>0): #todo: 
         print(out_paths['model_filepath'],idx)
-        io.save_models(models,out_paths['model_filepath'])
+        io.save_models_to_hdf5(models,out_paths['model_filepath'])
+
     if len(models)>0:
         # Generating the result table.
         table = io.generate_result_table(models,data_info)