fix abca script

openproblems-bio · Oct 1, 2024 · 4589ee4 · 4589ee4
1 parent d6ca3be
commit 4589ee4
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Showing 2 changed files with 18 additions and 12 deletions.
diff --git a/scripts/create_resources/process_allen_brain_cell_atlas_brain.sh b/scripts/create_resources/process_allen_brain_cell_atlas_brain.sh
@@ -18,10 +18,7 @@ param_list:
       - CTXsp
       - HPF
       - HY
-      - Isocortex-1
-      - Isocortex-2
-      - Isocortex-3
-      - Isocortex-4
+      - Isocortex
       - MB
       - OLF
       - TH

diff --git a/src/datasets/loaders/allen_brain_cell_atlas/script.py b/src/datasets/loaders/allen_brain_cell_atlas/script.py
@@ -4,11 +4,12 @@
 from collections import defaultdict
 import anndata as ad
 from abc_atlas_access.abc_atlas_cache.abc_project_cache import AbcProjectCache
+import re
 
 ## VIASH START
 par = {
     "abca_version": "20230630",
-    "regions": ["MB", "TF"],
+    "regions": ["MB", "TH"],
     "sample_n_obs": 5000,
     "sample_obs_weight": "subclass",
     "sample_transform": "sqrt",
@@ -76,13 +77,24 @@
 # TODO: potentially also load other chemistries (currently only 10Xv2)
 
 print("Downloading and reading expression matrices", flush=True)
+abca_data_subdir="WMB-10Xv2"
+abca_region_files = [
+    [file, region]
+    for file in abc_cache.list_data_files(abca_data_subdir)
+    for region in REGIONS
+    if re.match(f"WMB-10Xv2-{region}[\\-0-9]*/raw", file)
+]
+
 adatas = []
-for region in REGIONS:
+for region, abca_data_file in abca_region_files:
     try:
-        print(f"Downloading h5ad file for region {region}", flush=True)
-        adata_path = abc_cache.get_data_path(directory="WMB-10Xv2", file_name=f"WMB-10Xv2-{region}/raw")
+        print(f"Downloading file {abca_data_file} for region {region}", flush=True)
+        adata_path = abc_cache.get_data_path(
+            directory=abca_data_subdir,
+            file_name=abca_data_file
+        )
 
-        print(f"Reading h5ad for region {region}", flush=True)
+        print(f"Reading file {adata_path}", flush=True)
         adata = ad.read_h5ad(str(adata_path))
 
         if not par["keep_files"]:
@@ -91,9 +103,6 @@
         # filter cells
         adata = adata[adata.obs_names.isin(obs.index)].copy()
 
-        # add region to obs
-        adata.obs["region"] = region
-
         # move counts to layer
         adata.layers["counts"] = adata.X
         del adata.X