SURE-tools 2.1.79__py3-none-any.whl → 2.1.81__py3-none-any.whl

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 = int(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.dist-info → sure_tools-2.1.81.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.79
+Version: 2.1.81
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.79.dist-info → sure_tools-2.1.81.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=jvN2CD2L7YX6EiqP0Zw--zwegwHDiGkQYL2v_So5YYA,53382
+SURE/PerturbFlow.py,sha256=Hi7oF9S_eImo2Q-Oxu0mW461DHOG0O05TIE_pUW3uJo,54577
 SURE/SURE.py,sha256=g8EhovBxjfpbVJA0AkmVkQ_ZW_JFc8TtkTCg8FCybV4,47750
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -17,9 +17,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
 SURE/utils/custom_mlp.py,sha256=C0EXLGYsWkUQpEL49AyBFPSzKmasb2hdvtnJfxbF-YU,9282
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.79.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.79.dist-info/METADATA,sha256=B8i3DryW1NcFrOvzEROG5YDlZG14RHa_q2cVbNVUwmg,2678
-sure_tools-2.1.79.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.79.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.79.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.79.dist-info/RECORD,,
+sure_tools-2.1.81.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.81.dist-info/METADATA,sha256=uEiJyslzIPEZ_4HfoTR9JLtBuIfmAPH-HIu2Ar2dKg0,2678
+sure_tools-2.1.81.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.81.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.81.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.81.dist-info/RECORD,,