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Download and use new manifest.
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@morriscb
morriscb committed Nov 20, 2024
1 parent e04e6e0 commit 3645747
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Showing 2 changed files with 76 additions and 23 deletions.
51 changes: 39 additions & 12 deletions notebooks/Zeng_Aging_Mouse_10x_snRNASeq_tutorial.ipynb
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"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/allen/aibs/informatics/chris.morrison/miniconda/envs/abc_atlas_access/lib/python3.11/site-packages/abc_atlas_access/abc_atlas_cache/cloud_cache.py:470: MissingLocalManifestWarning: This cache directory appears to contain data files, but it has no record of what those files are. Unless running as a LocalCache, files will be re-downloaded.\n",
" warnings.warn(msg, MissingLocalManifestWarning)\n"
]
},
{
"data": {
"text/plain": [
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}
],
"source": [
"# download_base = Path('../../data/abc_atlas')\n",
"download_base = Path('/allen/programs/celltypes/workgroups/rnaseqanalysis/lydian/ABC_handoff')\n",
"abc_cache = AbcProjectCache.from_local_cache(download_base)\n",
"download_base = Path('../../data/abc_atlas')\n",
"abc_cache = AbcProjectCache.from_cache_dir(download_base)\n",
"\n",
"abc_cache.current_manifest"
]
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"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"gene.csv: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.30M/2.30M [00:00<00:00, 4.56MMB/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of genes = 32285\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"data": {
"text/html": [
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"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"example_genes_all_cells_expression.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 77.0M/77.0M [00:03<00:00, 22.0MMB/s]\n"
]
}
],
"source": [
"gene_names = ['Slc17a7', 'Slc17a6', 'Slc17a8', 'Slc32a1', 'Slc6a5', 'Slc6a3', 'Slc6a4', 'Tac2']\n",
"example_genes = abc_cache.get_metadata_dataframe(\n",
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"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"aging_degenes.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.13M/1.13M [00:00<00:00, 6.69MMB/s]\n"
]
},
{
"data": {
"text/html": [
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"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cluster_mapping_pivot.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 118k/118k [00:00<00:00, 854kMB/s]\n"
]
},
{
"data": {
"text/html": [
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48 changes: 37 additions & 11 deletions notebooks/Zeng_Aging_Mouse_clustering_analysis_and_annotation.ipynb
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Expand Up @@ -44,14 +44,6 @@
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/allen/aibs/informatics/chris.morrison/miniconda/envs/abc_atlas_access/lib/python3.11/site-packages/abc_atlas_access/abc_atlas_cache/cloud_cache.py:470: MissingLocalManifestWarning: This cache directory appears to contain data files, but it has no record of what those files are. Unless running as a LocalCache, files will be re-downloaded.\n",
" warnings.warn(msg, MissingLocalManifestWarning)\n"
]
},
{
"data": {
"text/plain": [
Expand All @@ -64,9 +56,8 @@
}
],
"source": [
"# download_base = Path('../../data/abc_atlas')\n",
"download_base = Path('/allen/programs/celltypes/workgroups/rnaseqanalysis/lydian/ABC_handoff')\n",
"abc_cache = AbcProjectCache.from_local_cache(download_base)\n",
"download_base = Path('../../data/abc_atlas')\n",
"abc_cache = AbcProjectCache.from_cache_dir(download_base)\n",
"\n",
"abc_cache.current_manifest"
]
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"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cell_metadata.csv: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 423M/423M [00:18<00:00, 22.3MMB/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
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"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cell_annotation_colors.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 76.1M/76.1M [00:03<00:00, 22.0MMB/s]\n"
]
},
{
"data": {
"text/html": [
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"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cluster.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 174k/174k [00:00<00:00, 1.17MMB/s]\n"
]
},
{
"data": {
"text/html": [
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"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cell_cluster_mapping_annotations.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 173M/173M [00:07<00:00, 22.7MMB/s]\n"
]
},
{
"data": {
"text/html": [
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"execution_count": 27,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cluster_mapping.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 405k/405k [00:00<00:00, 2.79MMB/s]\n"
]
},
{
"data": {
"text/html": [
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