add xenium

DendrouLab · Nov 11, 2024 · 9acc5d0 · 9acc5d0
1 parent ac41674
commit 9acc5d0
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/panpipes/funcs/io.py b/panpipes/funcs/io.py
@@ -156,6 +156,15 @@ def gen_load_spatial_jobs(caf, mode_dictionary = {}, load_raw=True):
                 spatial_filetype = None
             else:
                 spatial_path = caf["spatial_path"][nn]
+            if caf['spatial_filetype'][nn]=="xenium":
+                spatial_filetype = caf['spatial_filetype'][nn]
+                visium_feature_bc_matrix = None
+                visium_fullres_image_file = None
+                visium_tissue_positions_file = None
+                visium_scalefactors_file = None
+                vpt_cell_by_gene = None
+                vpt_cell_metadata = None
+                vpt_cell_boundaries = None
             if caf['spatial_filetype'][nn]=="vizgen":
                 visium_feature_bc_matrix = None 
                 visium_fullres_image_file = None

diff --git a/panpipes/python_scripts/make_spatialData_from_csv.py b/panpipes/python_scripts/make_spatialData_from_csv.py
@@ -155,7 +155,9 @@ def check_dir_transform(infile_path, transform_file):
                          tissue_positions_file=args.tissue_positions_file, 
                          scalefactors_file=args.scalefactors_file)
 
-
+elif args.spatial_filetype =="xenium": 
+    sdata = sd_io.xenium(path = args.spatial_infile)
+
 L.info("Resulting SpatialData is:")
 L.info(sdata)
 #L.info("Creating MuData with .mod['spatial']")