immucellai2 2.1.31__tar.gz → 2.1.33__tar.gz

{immucellai2-2.1.31 → immucellai2-2.1.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.31
+Version: 2.1.33
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.31 → immucellai2-2.1.33}/immucellai2/Deconvolution.py

@@ -256,17 +256,18 @@ def MainRun(RunObject, seed=42, MultithreadModule = 'joblib'):
     EnvironmentRun = RunObject.EnvironmentRun 
     RecordTime = CLASS_FOR_TIME() 
     nsamples = len(RunObject.SampleList) 
+    SampleNameToIndex = {name: idx for idx, name in enumerate(RunObject.SampleList)}
     parameterlist = []
-    #CelltypesReferenceMatrix = RunObject.CelltypesReferenceMatrix 
-    for sample_index in range(nsamples):
-        SampleName = RunObject.SampleList[sample_index]
+    for SampleNameii in range(nsamples):
+        SampleName = RunObject.SampleList[SampleNameii]
+        SampleIndex = SampleNameToIndex[SampleName]  
         parameterlist.append((
-            (RunObject.EmceeParameter).mycopy(),
-            RunObject.CelltypesReferenceMatrix ,
-            RunObject.SamplesBulkRNAseqExpression[sample_index],
-            RunObject.SampleList[sample_index], 
-            RunObject.MAPorMLE 
-        )) 
+            RunObject.EmceeParameter.mycopy(),
+            RunObject.CelltypesReferenceMatrix,
+            RunObject.SamplesBulkRNAseqExpression[SampleIndex],  
+            SampleName,
+            RunObject.MAPorMLE
+        ))
     MultiprocessingReturnValue = []
     if MultithreadModule == 'joblib':
        try:

{immucellai2-2.1.31 → immucellai2-2.1.33}/immucellai2/myclasses.py

@@ -99,16 +99,10 @@ class CLASS_FOR_RUNRESULT(object):
             self.EmceeFunction2( McSamplingResultList[sampleii, :, :, :] )
       return  NewMcSamplingResultList
    def optimized_calculation(self, FlatSamplingResultOne, nCellType):
-      row_sums = FlatSamplingResultOne.sum(axis=1, keepdims=True)
-      row_sums_safe = row_sums + 1e-10 
-      if FlatSamplingResultOne.shape[1] == nCellType:
-         return FlatSamplingResultOne / row_sums_safe
-      elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
-         normalized = FlatSamplingResultOne / row_sums_safe
-         last_col = 1 - normalized.sum(axis=1, keepdims=True)
-         return numpy.column_stack((normalized, last_col))
-      else:
-         raise ValueError(f"Dimension mismatch: input {FlatSamplingResultOne.shape[1]} columns, target {nCellType}columns")
+       if FlatSamplingResultOne.shape[1] == nCellType:
+           return FlatSamplingResultOne / FlatSamplingResultOne.sum(axis=1)[:, None]
+       elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
+           return numpy.column_stack((FlatSamplingResultOne, 1 - FlatSamplingResultOne.sum(axis=1)))
    def EmceeFunction2(self, FlatSamplingResultList): 
       fshape = FlatSamplingResultList.shape
       nCellType = len(self.CellType)

{immucellai2-2.1.31 → immucellai2-2.1.33}/immucellai2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.31
+Version: 2.1.33
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.31 → immucellai2-2.1.33}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = immucellai2
-version = 2.1.31
+version = 2.1.33
 author = YangJingmin
 author_email = yangjingmin2021@163.com
 description = A tool for immune cell type deconvolution