SURE-tools 2.1.79__tar.gz → 2.1.80__tar.gz

{sure_tools-2.1.79 → sure_tools-2.1.80}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.79
+Version: 2.1.80
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.79 → sure_tools-2.1.80}/SURE/PerturbFlow.py

@@ -807,6 +807,36 @@ class PerturbFlow(nn.Module):
         A = np.concatenate(A)
         return A
     
+    def predict(self, xs, us, perturbs_predict:list, perturbs_reference:list, library_sizes=None):
+        perturbs_reference = np.array(perturbs_reference)
+        
+        # basal embedding
+        zs = self.get_basal_embedding(xs)
+        for pert in perturbs_predict:
+            pert_idx = np.where(perturbs_reference==pert)[0]
+            us_i = us[:,pert_idx].reshape(-1,1)
+            
+            # factor effect of xs 
+            dzs0 = self.get_cell_response(xs, factor_idx=pert_idx, perturb=us_i)
+            
+            # perturbation effect 
+            ps = np.ones_like(us_i)
+            dzs = self.get_cell_response(xs, factor_idx=pert_idx, perturb=ps)
+            
+            zs = zs + dzs0 + dzs
+        
+        if library_sizes is None:
+            library_sizes = np.sum(xs, axis=1, keepdims=True)
+        elif type(library_sizes) == list:
+            library_sizes = np.array(library_sizes)
+            library_sizes = library_sizes.reshape(-1,1)
+        elif len(library_sizes.shape)==1:
+            library_sizes = library_sizes.reshape(-1,1)
+            
+        counts = self.get_counts(zs, library_sizes=library_sizes)
+        
+        return counts, zs
+    
     def _cell_response(self, xs, factor_idx, perturb):
         #zns,_ = self.encoder_zn(xs)    
         zns,_ = self._get_basal_embedding(xs)   

{sure_tools-2.1.79 → sure_tools-2.1.80}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.79
+Version: 2.1.80
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.79 → sure_tools-2.1.80}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.79',
+    version='2.1.80',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",