From 06b44c97d2ed20858d758a25e9060e0e167acda5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Oct 2024 15:45:23 +0200 Subject: [PATCH] fix component --- .../loaders/allen_brain_cell_atlas/config.vsh.yaml | 5 +---- src/datasets/loaders/allen_brain_cell_atlas/script.py | 8 ++++---- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/src/datasets/loaders/allen_brain_cell_atlas/config.vsh.yaml b/src/datasets/loaders/allen_brain_cell_atlas/config.vsh.yaml index 0e8ddcad..ff7e32fb 100644 --- a/src/datasets/loaders/allen_brain_cell_atlas/config.vsh.yaml +++ b/src/datasets/loaders/allen_brain_cell_atlas/config.vsh.yaml @@ -18,10 +18,7 @@ argument_groups: - 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 index 42e16dcb..6255e46b 100644 --- a/src/datasets/loaders/allen_brain_cell_atlas/script.py +++ b/src/datasets/loaders/allen_brain_cell_atlas/script.py @@ -79,19 +79,19 @@ print("Downloading and reading expression matrices", flush=True) abca_data_subdir="WMB-10Xv2" abca_region_files = [ - [file, region] + [re.sub(r"/raw$", "", 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, abca_data_file in abca_region_files: +for region, file_name in abca_region_files: try: - print(f"Downloading file {abca_data_file} for region {region}", flush=True) + print(f"Downloading file {file_name} for region {region}", flush=True) adata_path = abc_cache.get_data_path( directory=abca_data_subdir, - file_name=abca_data_file + file_name=file_name ) print(f"Reading file {adata_path}", flush=True)