change function and parameter names

panpipes/panpipes/pipeline_preprocess_spatial.py

@@ -52,7 +52,7 @@ def gen_filter_jobs():
 @mkdir("tables")
 @mkdir("filtered.data")
 @files(gen_filter_jobs)
-def filter_mudata(infile_path,outfile):
+def filter_spatialdata(infile_path,outfile):
     print('processing file = %s' % str(infile_path))
     log_file = os.path.basename(outfile)
     log_file= "1_filtering."+log_file.replace("filtered.zarr","") + ".log"
@@ -61,15 +61,15 @@ def filter_mudata(infile_path,outfile):
     filter_dict = dictionary_stripper(PARAMS['filtering'])
     cmd = """
         python %(py_path)s/run_filter_spatial.py
-        --input_mudata %(infile_path)s
-        --output_mudata %(outfile)s
+        --input_spatialdata %(infile_path)s
+        --output_spatialdata %(outfile)s
         --filter_dict "%(filter_dict)s"
         """
     if PARAMS['filtering_keep_barcodes'] is not None:
         cmd += " --keep_barcodes %(filtering_keep_barcodes)s"
     cmd += " > logs/%(log_file)s "
     job_kwargs["job_threads"] = PARAMS['resources_threads_low']
-    log_msg = f"TASK: 'filter_mudata'" + f" IN CASE OF ERROR, PLEASE REFER TO : 'logs/{log_file}' FOR MORE INFORMATION."
+    log_msg = f"TASK: 'filter_spatialdata'" + f" IN CASE OF ERROR, PLEASE REFER TO : 'logs/{log_file}' FOR MORE INFORMATION."
     get_logger().info(log_msg)
     P.run(cmd, **job_kwargs)
 
@@ -84,7 +84,7 @@ def run_plotqc_query(pqc_dict):
 
 @active_if(run_plotqc_query(PARAMS['plotqc']))
 @active_if(PARAMS['filtering_run'])
-@transform(filter_mudata,
+@transform(filter_spatialdata,
            regex("./filtered.data/(.*)_filtered.zarr"), 
            r"./logs/2_postfilterplot.\1.log")
 def postfilterplot_spatial(filt_file,log_file):
@@ -93,7 +93,7 @@ def postfilterplot_spatial(filt_file,log_file):
     spatial_filetype = PARAMS["assay"]
     cmd = """
             python %(py_path)s/plot_qc_spatial.py
-             --input_mudata %(filt_file)s
+             --input_spatialdata %(filt_file)s
              --spatial_filetype %(spatial_filetype)s
              --figdir ./figures/spatial
             """
@@ -108,7 +108,7 @@ def postfilterplot_spatial(filt_file,log_file):
     P.run(cmd, **job_kwargs)
 
 
-@transform(filter_mudata,
+@transform(filter_spatialdata,
            regex("./filtered.data/(.*)_filtered.zarr"), 
            r"./logs/3_preprocess.\1.log")
 def spatial_preprocess(filt_file,log_file):
@@ -119,8 +119,8 @@ def spatial_preprocess(filt_file,log_file):
     write_output = os.path.join("./tmp/",os.path.basename(filt_file))
     cmd = """
         python %(py_path)s/run_preprocess_spatial.py
-        --input_mudata %(filt_file)s
-        --output_mudata %(write_output)s
+        --input_spatialdata %(filt_file)s
+        --output_spatialdata %(write_output)s
         --figdir ./figures/spatial
         """
     if PARAMS['spatial_norm_hvg_flavour'] is not None:
@@ -154,7 +154,7 @@ def spatial_preprocess(filt_file,log_file):
     get_logger().info(log_msg)
     P.run(cmd, **job_kwargs)
 
-@follows(filter_mudata, postfilterplot_spatial, spatial_preprocess)
+@follows(filter_spatialdata, postfilterplot_spatial, spatial_preprocess)
 @originate("cleanup_done.txt")
 def cleanup(file):
     # remove any ctmp fails

panpipes/panpipes/pipeline_qc_spatial.py

@@ -56,7 +56,7 @@ def set_up_dirs(log_file):
     pass
 
 # -----------------------------------------------------------------------------------------------
-## Creating h5mu from filtered data files
+## Creating spatialData from filtered data files
 # -----------------------------------------------------------------------------------------------
 
 
@@ -73,7 +73,7 @@ def gen_load_spatial_anndata_jobs():
 @follows(mkdir("logs"))
 @follows(mkdir("tmp"))
 @files(gen_load_spatial_anndata_jobs)
-def load_mudatas(spatial_path,  outfile, 
+def load_spatialdatas(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):
 
@@ -119,19 +119,19 @@ def load_mudatas(spatial_path,  outfile,
         --vpt_cell_metadata %(vpt_cell_metadata)s 
         --vpt_cell_boundaries %(vpt_cell_boundaries)s
         """
-    cmd += " > logs/1_make_mudatas_%(sample_id)s.log"
+    cmd += " > logs/1_make_spatialdatas_%(sample_id)s.log"
     job_kwargs["job_threads"] = PARAMS['resources_threads_medium']
-    log_msg = f"TASK: 'load_mudatas'" + f" IN CASE OF ERROR, PLEASE REFER TO : 'logs/1_make_mudatas_{sample_id}.log' FOR MORE INFORMATION."
+    log_msg = f"TASK: 'load_spatialdatas'" + f" IN CASE OF ERROR, PLEASE REFER TO : 'logs/1_make_spatialdatas_{sample_id}.log' FOR MORE INFORMATION."
     get_logger().info(log_msg)
     P.run(cmd, **job_kwargs)
 
 
 
 
-@follows(load_mudatas)
+@follows(load_spatialdatas)
 @follows(mkdir("qc.data"))
 @follows(mkdir("./figures"))
-@transform(load_mudatas,
+@transform(load_spatialdatas,
            regex("./tmp/(.*)_raw.zarr"), 
            r"./logs/2_spatialQC_\1.log")
 def spatialQC(infile,log_file):
@@ -179,7 +179,7 @@ def run_plotqc_query(pqc_dict):
 @follows(spatialQC)
 @follows(mkdir("./figures/spatial"))
 @active_if(run_plotqc_query(PARAMS['plotqc']))
-@transform(load_mudatas, 
+@transform(load_spatialdatas, 
            regex("./tmp/(.*)_raw.zarr"),
            r"./logs/3_qcplot.\1.log")
 def plotQC_spatial(unfilt_file,log_file):
@@ -188,7 +188,7 @@ def plotQC_spatial(unfilt_file,log_file):
     unfilt_file = unfilt_file.replace("tmp", "qc.data")
     cmd = """
             python %(py_path)s/plot_qc_spatial.py
-             --input_mudata %(unfilt_file)s
+             --input_spatialdata %(unfilt_file)s
              --spatial_filetype %(spatial_filetype)s
              --figdir ./figures/spatial
             """

panpipes/python_scripts/plot_qc_spatial.py

@@ -28,8 +28,8 @@
 
 parser = argparse.ArgumentParser()
 
-parser.add_argument("--input_mudata",
-                    default="mudata_unfilt.h5mu",
+parser.add_argument("--input_spatialdata",
+                    default="spatialdata_unfilt.h5mu",
                     help="")
 parser.add_argument("--figdir",
                     default="./figures/",
@@ -58,12 +58,12 @@
 sc.settings.figdir = figdir
 sc.set_figure_params(scanpy=True, fontsize=14, dpi=300, facecolor='white', figsize=(5,5))
 
-L.info("Reading in SpatialData from '%s'" % args.input_mudata)
-sdata = sd.read_zarr(args.input_mudata)
-#mdata = mu.read(args.input_mudata)
+L.info("Reading in SpatialData from '%s'" % args.input_spatialdata)
+sdata = sd.read_zarr(args.input_spatialdata)
+#mdata = mu.read(args.input_spatialdata)
 #spatial = mdata.mod['spatial']
 
-input_data = os.path.basename(args.input_mudata)
+input_data = os.path.basename(args.input_spatialdata)
 pattern = r"_filtered.zarr"
 match = re.search(pattern, input_data)
 if match is None:

panpipes/python_scripts/run_filter_spatial.py

@@ -42,18 +42,18 @@ def test_matching_df_ignore_cat(new_df, old_df):
 # parse arguments
 parser = argparse.ArgumentParser()
 
-parser.add_argument('--input_mudata',
+parser.add_argument('--input_spatialdata',
                     default='gut_minus1_amp.h5ad',
                     help='')
-parser.add_argument('--output_mudata',
+parser.add_argument('--output_spatialdata',
                     default='',
                     help='')
 parser.add_argument('--filter_dict',
                     default='',
                     help='this is pull')
 # cross modalities args
 parser.add_argument('--keep_barcodes', default=None,
-                    help='1 column list of barcodes to keep, note that they should match the mudata input, this filtering happens first')
+                    help='1 column list of barcodes to keep, note that they should match the spatialdata input, this filtering happens first')
 
 
 # load options
@@ -73,14 +73,14 @@ def test_matching_df_ignore_cat(new_df, old_df):
 filter_dict = dictionary_stripper(filter_dict)
 L.info("Filter dictionary:\n %s" %filter_dict)
 
-# load mudata
+# load spatialdata
 
-L.info("Reading in SpatialData from '%s'" % args.input_mudata)
-sdata = sd.read_zarr(args.input_mudata)
-#mdata = mu.read(args.input_mudata)
+L.info("Reading in SpatialData from '%s'" % args.input_spatialdata)
+sdata = sd.read_zarr(args.input_spatialdata)
+#mdata = mu.read(args.input_spatialdata)
 
 #if isinstance(mdata, AnnData):
-#    raise TypeError("Input '%s' should be of MuData format, not Anndata"  % args.input_mudata)
+#    raise TypeError("Input '%s' should be of spatialdata format, not Anndata"  % args.input_spatialdata)
 
 orig_obs = sdata["table"].obs.copy()
 
@@ -147,7 +147,7 @@ def test_matching_df_ignore_cat(new_df, old_df):
 assert test_matching_df_ignore_cat(sdata["table"].obs, orig_obs)  
 
 # write out obs
-output_prefix = re.sub(".zarr", "", os.path.basename(args.output_mudata))
+output_prefix = re.sub(".zarr", "", os.path.basename(args.output_spatialdata))
 
 L.info("Saving updated obs in a metadata tsv file to './tables/" + output_prefix + "_filtered_cell_metadata.tsv'")
 write_obs(sdata["table"], output_prefix=os.path.join("tables/",output_prefix), output_suffix="_filtered_cell_metadata.tsv")
@@ -166,8 +166,8 @@ def test_matching_df_ignore_cat(new_df, old_df):
 
 #mdata.update()
 
-L.info("Saving updated SpatialData to '%s'" % args.output_mudata)
-sdata.write(args.output_mudata)
+L.info("Saving updated SpatialData to '%s'" % args.output_spatialdata)
+sdata.write(args.output_spatialdata)
 
 L.info("Done")
 

panpipes/python_scripts/run_preprocess_spatial.py

@@ -32,11 +32,11 @@
 
 parser = argparse.ArgumentParser()
 
-parser.add_argument("--input_mudata",
-                    default="mudata_unfilt.h5mu",
+parser.add_argument("--input_spatialdata",
+                    default="spatialdata_unfilt.h5mu",
                     help="")
-parser.add_argument("--output_mudata",
-                    default="mudata_unfilt.h5mu",
+parser.add_argument("--output_spatialdata",
+                    default="spatialdata_unfilt.h5mu",
                     help="")
 parser.add_argument("--figdir",
                     default="./figures/",
@@ -89,12 +89,12 @@
 sc.settings.figdir = figdir
 sc.set_figure_params(scanpy=True, fontsize=14, dpi=300, facecolor='white', figsize=(5,5))
 
-L.info("Reading in SpatialData from '%s'" % args.input_mudata)
-sdata = sd.read_zarr(args.input_mudata)
-#mdata = mu.read(args.input_mudata)
+L.info("Reading in SpatialData from '%s'" % args.input_spatialdata)
+sdata = sd.read_zarr(args.input_spatialdata)
+#mdata = mu.read(args.input_spatialdata)
 #spatial = mdata.mod['spatial']
 
-input_data = os.path.basename(args.input_mudata)
+input_data = os.path.basename(args.input_spatialdata)
 pattern = r"_filtered.zarr"
 match = re.search(pattern, input_data)
 sprefix = input_data[:match.start()]
@@ -174,8 +174,8 @@
 
 
 #mdata.update()
-L.info("Saving updated SpatialData to '%s'" % args.output_mudata)
-sdata.write(args.output_mudata)
+L.info("Saving updated SpatialData to '%s'" % args.output_spatialdata)
+sdata.write(args.output_spatialdata)
 
 L.info("Done")