SURE-tools 2.0.10__py3-none-any.whl → 2.1.0__py3-none-any.whl

SURE/SURE.py

@@ -813,77 +813,6 @@ class SURE(nn.Module):
         A = np.concatenate(A)
         return A
     
-    def _cell_move(self, xs, factor_idx, perturb):
-        zns,_ = self.encoder_zn(xs)
-        if type(factor_idx) == str:
-            factor_idx = int(np.where(self.cell_factor_names==factor_idx)[0])
-        
-        if perturb.ndim==2:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb])
-        else:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb.reshape(-1,1)])
-            
-        return ms 
-
-    def get_cell_move(self, 
-                             xs, 
-                             factor_idx,
-                             perturb,
-                             batch_size: int = 1024):
-        """
-        Return cells' changes in the latent space induced by specific perturbation of a factor
-
-        """
-        xs = self.preprocess(xs)
-        xs = convert_to_tensor(xs, device=self.get_device())
-        ps = convert_to_tensor(perturb, device=self.get_device())
-        dataset = CustomDataset2(xs,ps)
-        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
-
-        Z = []
-        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for X_batch, P_batch, _ in dataloader:
-                zns = self._cell_move(X_batch, factor_idx, P_batch)
-                Z.append(tensor_to_numpy(zns))
-                pbar.update(1)
-
-        Z = np.concatenate(Z)
-        return Z
-    
-    def get_metacell_move(self, factor_idx, perturb):
-        zs = self._get_codebook()
-        ps = convert_to_tensor(perturb, device=self.get_device())
-        
-        if type(factor_idx) == str:
-            factor_idx = int(np.where(self.cell_factor_names==factor_idx)[0])
-            
-        ms = self.cell_factor_effect[factor_idx]([zs,ps])
-        return tensor_to_numpy(ms)
-    
-    def _get_expression_responses(self, delta_zs):
-        return self.decoder_concentrate(delta_zs)
-    
-    def get_expression_responses(self, 
-                             delta_zs, 
-                             batch_size: int = 1024):
-        """
-        Return cells' changes in the latent space induced by specific perturbation of a factor
-
-        """
-        delta_zs = convert_to_tensor(delta_zs, device=self.get_device())
-        dataset = CustomDataset(delta_zs)
-        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
-
-        R = []
-        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for delta_Z_batch, _ in dataloader:
-                r = self._cell_move(delta_Z_batch)
-                R.append(tensor_to_numpy(r))
-                pbar.update(1)
-
-        R = np.concatenate(R)
-        return R
-    
     def preprocess(self, xs, threshold=0):
         if self.loss_func == 'bernoulli':
             ad = sc.AnnData(xs)

SURE/__init__.py

@@ -1,10 +1,11 @@
 from .SURE import SURE
-from .SURE2 import SURE2
+from .PerturbFlow import PerturbFlow
 
 from . import utils 
 from . import codebook
 from . import SURE
+from . import PerturbFlow
 from . import atac
 from . import flow 
 
-__all__ = ['SURE', 'flow', 'atac', 'utils', 'codebook']
+__all__ = ['SURE', 'PerturbFlow', 'flow', 'atac', 'utils', 'codebook']

{sure_tools-2.0.10.dist-info → sure_tools-2.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.10
+Version: 2.1.0
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.10.dist-info → sure_tools-2.1.0.dist-info}/RECORD

@@ -1,6 +1,7 @@
-SURE/SURE.py,sha256=DzuRXp9AtnwoezsR-zTkm6PxlfOV8sdmu3mYwkapYQs,51875
+SURE/PerturbFlow.py,sha256=ko6DcOoO-IUEm736n689jmtJSHM_s2hafG-yUmflNSU,52019
+SURE/SURE.py,sha256=OmwmA8RnhwrirXgnzqJMxv1BCr1jmjfHitvlmBKhHNA,49245
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
-SURE/__init__.py,sha256=mxdLoWa2fPEM4-WkJetMfcecpzqJ8YsM4lOoKHSLTrU,207
+SURE/__init__.py,sha256=xV10iBbh69g4mjBMb1cQxjuHe8e3Aq7pDzkZmx5G754,260
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
 SURE/assembly/atlas.py,sha256=ALjmVWutm_tOHTcT1aqOxmuCEQw-XzrtDoMCV_8oXLk,21794
@@ -15,9 +16,9 @@ SURE/utils/__init__.py,sha256=Htqv4KqVKcRiaaTBsR-6yZ4LSlbhbzutjNKXGD9-uds,660
 SURE/utils/custom_mlp.py,sha256=07TYX1HgxfEjb_3i5MpiZfNhOhx3dKntuwGkrpteWiM,7036
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.0.10.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.0.10.dist-info/METADATA,sha256=_64vkwUxRdYs5xvh76oYB34PUDpEnCN5Inl5tlGhe38,2651
-sure_tools-2.0.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.0.10.dist-info/entry_points.txt,sha256=u12payZYgCBy5FCwRHP6AlSQhKCiWSEDwj68r1DVdn8,40
-sure_tools-2.0.10.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.0.10.dist-info/RECORD,,
+sure_tools-2.1.0.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.0.dist-info/METADATA,sha256=bH8ARqqdk2bnLC5rk8MvPgBVAb8kaEKnzuHwyyDXpvE,2650
+sure_tools-2.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.0.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.0.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.0.dist-info/RECORD,,

sure_tools-2.1.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+PerturbFlow = PerturbFlow.PerturbFlow:main
+SURE = SURE.SURE:main

sure_tools-2.0.10.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-SURE = SURE.SURE:main