immucellai2 2.1.28__tar.gz → 2.1.29__tar.gz

{immucellai2-2.1.28 → immucellai2-2.1.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.28
+Version: 2.1.29
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.28 → immucellai2-2.1.29}/immucellai2/PrepareData.py

@@ -8,33 +8,18 @@ import sys
 import multiprocessing as mp
 
 def SelectGeneForDeconvolution(DFReferenceProfile, FileCoveredGenes="", Method="UsedMarker"):
-   print("Select the gene for the following deconvolution...")
-   GeneUsedForDeconvolution = []
-   DFReferenceProfileGenes = DFReferenceProfile.index.values
-   if Method == "UsedMarker":
-      if FileCoveredGenes == "": 
-         try:
-            marker_path = files("immucellai2.myconfig").joinpath("MarkerUsedDeconvolution.txt")
-            FileCoveredGenes = str(marker_path)
-         except Exception as e:
-            script_dir = os.path.dirname(os.path.abspath(sys.argv[0]))
-            FileCoveredGenes = os.path.join(script_dir, "immucellai2/myconfig/MarkerUsedDeconvolution.txt")
-            print(f"[WARNING] Using fallback path: {FileCoveredGenes}")
-      try:
-         GeneUsedForDeconvolution0 = pandas.read_table(FileCoveredGenes, sep="\t", header=None).iloc[1].tolist()
-         print(f"[DEBUG] head:\n list(islice(GeneUsedForDeconvolution0, 3))")
-         GeneUsedForDeconvolution = list(set(GeneUsedForDeconvolution0).intersection(set(DFReferenceProfileGenes)))
-         print(f"Successfully loaded {len(GeneUsedForDeconvolution)} marker genes")
-      except FileNotFoundError:
-         print(f"Error: Marker file not found - {FileCoveredGenes}")
-         print("Please check:")
-         print("1. Package is installed correctly (pip install --upgrade immucellai2)")
-         print("2. Environment variable IMMUCELLAI_CONFIG_DIR is set")
-         return [] 
-      except Exception as e:
-         print(f"Error reading marker file: {str(e)}") 
-         return [] 
-   return GeneUsedForDeconvolution
+    print("Select the gene for the following deconvolution...")
+    GeneUsedForDeconvolution = []
+    DFReferenceProfileGenes = DFReferenceProfile.index.values
+    if Method == "UsedMarker":
+        if FileCoveredGenes == "":
+            pkg_marker_path = os.path.join(get_package_dir("immucellai2"), "myconfig/MarkerUsedDeconvolution.txt")
+            if os.path.exists(pkg_marker_path):
+                FileCoveredGenes = pkg_marker_path
+                print(f"[INFO] Found marker file in immucellai2 package: {FileCoveredGenes}")
+            GeneUsedForDeconvolution0 = (pandas.read_table(FileCoveredGenes, sep= "\t")).iloc[0].to_list()
+            GeneUsedForDeconvolution = list(set(GeneUsedForDeconvolution0).intersection(set(DFReferenceProfileGenes)))
+    return GeneUsedForDeconvolution
 
 def Obtainmyconfigpath():
    script_dir = os.path.dirname(os.path.abspath(sys.argv[0]))

{immucellai2-2.1.28 → immucellai2-2.1.29}/immucellai2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.28
+Version: 2.1.29
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.28 → immucellai2-2.1.29}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = immucellai2
-version = 2.1.28
+version = 2.1.29
 author = YangJingmin
 author_email = yangjingmin2021@163.com
 description = A tool for immune cell type deconvolution