immucellai2 2.1.28__py3-none-any.whl → 2.1.30__py3-none-any.whl

immucellai2/PrepareData.py

@@ -6,35 +6,28 @@ import os
 import re
 import sys
 import multiprocessing as mp
+import importlib.util
+
+def get_package_dir(package_name):
+    spec = importlib.util.find_spec(package_name)
+    if spec is None:
+        raise ModuleNotFoundError(f"Package '{package_name}' not found")
+    path = spec.origin or spec.submodule_search_locations[0]
+    return os.path.dirname(path)
 
 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.dist-info → immucellai2-2.1.30.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.28
+Version: 2.1.30
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.28.dist-info → immucellai2-2.1.30.dist-info}/RECORD

@@ -1,7 +1,7 @@
 immucellai2/Deconvolution.py,sha256=8fYLWKHFf1qahY7qEt5nnsrju7S7kF9f2ch3YXaKQMU,12577
 immucellai2/Drawplot.py,sha256=YnUleceEyim9SsTiU18mbAMcjOH9ovBXJW3pwXxA7as,5136
 immucellai2/ObtainCategory.py,sha256=N1F_yUHoaIisnlms4aNNJ2UIzZDI2TIc0t7IRLtM7So,7008
-immucellai2/PrepareData.py,sha256=bV0H7OVVuB-BOcQqQazaYpE4RbB9uk8rVXQPrnYhZ5Q,6359
+immucellai2/PrepareData.py,sha256=tJWtQbfFfXszAQMnAmyzFrXB40wgHl48WP3WZKfeifg,5935
 immucellai2/Time.py,sha256=et3aAqyVDKwP5_tdGIwA6yxdXRbbYemc9wEaPHpQCck,572
 immucellai2/__init__.py,sha256=wi7UznfkskCvT4yj-u1RuyN0SK1tZptpXffIaQW2XkQ,3055
 immucellai2/myclasses.py,sha256=9Rgil00HX_RfOhvpdvUZDsvFi7RdIfXay4V3lRcQsQ8,12409
@@ -9,8 +9,8 @@ immucellai2/myconfig/Celltype.category,sha256=l_5vspGpyDbuaQ7QOLIQjSs4xb6x6_pvvt
 immucellai2/myconfig/MarkerUsedDeconvolution.txt,sha256=33gCFD1_Clis7NFaQTUHc5s7BXoN61jWgWPgjT-m0n0,60756
 immucellai2/myconfig/reference_normalCelltypes.txt,sha256=zhKP5Z1TgVyB6ijIamjM1ETmuwQgRATofO-0ds89gP4,39107049
 immucellai2/myconfig/reference_tumorCelltypes.txt,sha256=xYgjehHIXb5re20bmXeoqxfyvQmgpr4y-0ysCVnEeI8,40893156
-immucellai2-2.1.28.dist-info/METADATA,sha256=QYja6j1Cya9QA7p6jnbgwBUrOpmWDVgyRDJaeypWbIg,1662
-immucellai2-2.1.28.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-immucellai2-2.1.28.dist-info/entry_points.txt,sha256=asskhaErD37JB_X_4TPB1itaIytWCU-RHFIyVGQ8Jbw,62
-immucellai2-2.1.28.dist-info/top_level.txt,sha256=9r84YbXmTdnKZnK2OGrTsgYPFoSBdk4EkeieDg-7_DY,12
-immucellai2-2.1.28.dist-info/RECORD,,
+immucellai2-2.1.30.dist-info/METADATA,sha256=NKn592muAUBDhIluHj7pKTLUOrdpNxGwXGn64E_fpKQ,1662
+immucellai2-2.1.30.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+immucellai2-2.1.30.dist-info/entry_points.txt,sha256=asskhaErD37JB_X_4TPB1itaIytWCU-RHFIyVGQ8Jbw,62
+immucellai2-2.1.30.dist-info/top_level.txt,sha256=9r84YbXmTdnKZnK2OGrTsgYPFoSBdk4EkeieDg-7_DY,12
+immucellai2-2.1.30.dist-info/RECORD,,