add vpt parameters

panpipes/funcs/io.py

@@ -157,40 +157,58 @@ def gen_load_spatial_jobs(caf, mode_dictionary = {}, load_raw=True):
             else:
                 spatial_path = caf["spatial_path"][nn]
             if caf['spatial_filetype'][nn]=="vizgen":
-                spatial_counts = None 
-                spatial_fullres_image_file = None
-                spatial_tissue_positions_file = None
-                spatial_scalefactors_file = None
+                visium_feature_bc_matrix = None 
+                visium_fullres_image_file = None
+                visium_tissue_positions_file = None
+                visium_scalefactors_file = None
                 spatial_filetype = caf['spatial_filetype'][nn]
+                if pd.notna(caf['vpt_cell_by_gene'][nn]):
+                    vpt_cell_by_gene = caf['vpt_cell_by_gene'][nn]
+                else:
+                    vpt_cell_by_gene = None
+                if pd.notna(caf['vpt_cell_metadata'][nn]):
+                    vpt_cell_metadata = caf['vpt_cell_metadata'][nn]
+                else:
+                    vpt_cell_metadata = None
+                if pd.notna(caf['vpt_cell_boundaries'][nn]):
+                    vpt_cell_boundaries = caf['vpt_cell_boundaries'][nn]
+                else:
+                    vpt_cell_boundaries = None
             elif caf['spatial_filetype'][nn]=="visium":
+                vpt_cell_by_gene = None
+                vpt_cell_metadata = None
+                vpt_cell_boundaries = None
                 spatial_filetype = caf['spatial_filetype'][nn]
                 #counts file
-                if pd.notna(caf["spatial_counts"][nn]):
-                    spatial_counts= caf["spatial_counts"][nn]
+                if pd.notna(caf["visium_feature_bc_matrix"][nn]):
+                    visium_feature_bc_matrix= caf["visium_feature_bc_matrix"][nn]
                 else:
-                    spatial_counts = None  
+                    visium_feature_bc_matrix = None  
                 # fullres image
-                if pd.notna(caf["spatial_fullres_image_file"][nn]):
-                    spatial_fullres_image_file= caf["spatial_fullres_image_file"][nn]
+                if pd.notna(caf["visium_fullres_image_file"][nn]):
+                    visium_fullres_image_file= caf["visium_fullres_image_file"][nn]
                 else:
-                    spatial_fullres_image_file = None 
+                    visium_fullres_image_file = None 
                 # tissue position 
-                if pd.notna(caf["spatial_tissue_positions_file"][nn]):
-                    spatial_tissue_positions_file= caf["spatial_tissue_positions_file"][nn]
+                if pd.notna(caf["visium_tissue_positions_file"][nn]):
+                    visium_tissue_positions_file= caf["visium_tissue_positions_file"][nn]
                 else:
-                    spatial_tissue_positions_file = None  
+                    visium_tissue_positions_file = None  
                 # scalefactor
-                if pd.notna(caf["spatial_scalefactors_file"][nn]):
-                    spatial_scalefactors_file= caf["spatial_scalefactors_file"][nn]
+                if pd.notna(caf["visium_scalefactors_file"][nn]):
+                    visium_scalefactors_file= caf["visium_scalefactors_file"][nn]
                 else:
-                    spatial_scalefactors_file = None  
+                    visium_scalefactors_file = None  
         else:
             spatial_path= None
             spatial_filetype = None
-            spatial_counts = None
-            spatial_fullres_image_file = None
-            spatial_tissue_positions_file = None
-            spatial_scalefactors_file = None
+            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 'barcode_mtd_path' in caf.columns:
             cell_mtd_path = caf['barcode_mtd_path'][nn] #not yielding this right now!
@@ -204,8 +222,9 @@ def gen_load_spatial_jobs(caf, mode_dictionary = {}, load_raw=True):
             outfile = outfile + ".zarr"
         sample_id = caf['sample_id'][nn]
 
-        yield spatial_path,  outfile, \
-              sample_id, spatial_filetype, spatial_counts, spatial_fullres_image_file, spatial_tissue_positions_file, spatial_scalefactors_file
+        yield spatial_path, outfile, sample_id, spatial_filetype, \
+              visium_feature_bc_matrix, visium_fullres_image_file, visium_tissue_positions_file, visium_scalefactors_file, \
+              vpt_cell_by_gene, vpt_cell_metadata, vpt_cell_boundaries
 
 
 def read_anndata(

panpipes/panpipes/pipeline_qc_spatial.py

@@ -74,26 +74,25 @@ def gen_load_spatial_anndata_jobs():
 @follows(mkdir("tmp"))
 @files(gen_load_spatial_anndata_jobs)
 def load_mudatas(spatial_path,  outfile, 
-                 sample_id, spatial_filetype, spatial_counts, 
-                 spatial_fullres_image_file, spatial_tissue_positions_file, spatial_scalefactors_file):
+                 sample_id, spatial_filetype, visium_feature_bc_matrix, visium_fullres_image_file, visium_tissue_positions_file, visium_scalefactors_file,
+              vpt_cell_by_gene, vpt_cell_metadata, vpt_cell_boundaries):
 
     path_dict = {'spatial':spatial_path}
 
     print(path_dict)
     print('sample_id = %s' % str(sample_id))
     print('outfile = %s' % str(outfile))
     print('spatial_filetype = %s' % str(spatial_filetype))
-    #print('spatial_counts = %s' % str(spatial_counts))
-    #if spatial_filetype == "vizgen":
-    #    print('spatial_metadata = %s' % str(spatial_metadata))
-    #    print('spatial_transformation = %s' % str(spatial_transformation))
-    #else:
-    #    print("visium")
+
     if spatial_filetype == "visium":
-        print('spatial_counts = %s' % str(spatial_counts))
-        print('spatial_fullres_image_file= %s' % str(spatial_fullres_image_file))
-        print('spatial_tissue_positions_file= %s' % str(spatial_tissue_positions_file))
-        print('spatial_scalefactors_file= %s' % str(spatial_scalefactors_file))
+        print('visium_feature_bc_matrix = %s' % str(visium_feature_bc_matrix))
+        print('visium_fullres_image_file= %s' % str(visium_fullres_image_file))
+        print('visium_tissue_positions_file= %s' % str(visium_tissue_positions_file))
+        print('visium_scalefactors_file= %s' % str(visium_scalefactors_file))
+    if spatial_filetype == "vizgen":
+        print('vpt_cell_by_gene = %s' % str(vpt_cell_by_gene))
+        print('vpt_cell_metadata= %s' % str(vpt_cell_metadata))
+        print('vpt_cell_boundaries= %s' % str(vpt_cell_boundaries))
     modality_dict = {k:True if path_dict[k] is not None else False for k,v in {'spatial': True}.items() }
     print(modality_dict)
 
@@ -109,10 +108,16 @@ def load_mudatas(spatial_path,  outfile,
     """
     if spatial_filetype == "visium":
         cmd += """
-        --spatial_counts %(spatial_counts)s
-        --scalefactors_file %(spatial_scalefactors_file)s 
-        --fullres_image_file %(spatial_fullres_image_file)s
-        --tissue_positions_file %(spatial_tissue_positions_file)s
+        --visium_feature_bc_matrix %(visium_feature_bc_matrix)s
+        --scalefactors_file %(visium_scalefactors_file)s 
+        --fullres_image_file %(visium_fullres_image_file)s
+        --tissue_positions_file %(visium_tissue_positions_file)s
+        """
+    if spatial_filetype == "vizgen":
+        cmd += """
+        --vpt_cell_by_gene %(vpt_cell_by_gene)s
+        --vpt_cell_metadata %(vpt_cell_metadata)s 
+        --vpt_cell_boundaries %(vpt_cell_boundaries)s
         """
     cmd += " > logs/1_make_mudatas_%(sample_id)s.log"
     job_kwargs["job_threads"] = PARAMS['resources_threads_medium']