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scgpt filemodel is added
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@janursa
janursa committed Nov 26, 2024
1 parent cea9362 commit 608673a
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Showing 3 changed files with 8 additions and 69 deletions.
62 changes: 0 additions & 62 deletions runs.ipynb
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Expand Up @@ -46,68 +46,6 @@
"# !aws s3 sync resources/ s3://openproblems-data/resources/grn/ --delete"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"File downloaded successfully and saved to output//args.json\n"
]
},
{
"ename": "JSONDecodeError",
"evalue": "Expecting value: line 1 column 1 (char 0)",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mJSONDecodeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[4], line 31\u001b[0m\n\u001b[1;32m 29\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mjson\u001b[39;00m\n\u001b[1;32m 30\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(par[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmodel_config_file\u001b[39m\u001b[38;5;124m'\u001b[39m]) \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[0;32m---> 31\u001b[0m \u001b[43mjson\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mload\u001b[49m\u001b[43m(\u001b[49m\u001b[43mf\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/py10/lib/python3.10/json/__init__.py:293\u001b[0m, in \u001b[0;36mload\u001b[0;34m(fp, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)\u001b[0m\n\u001b[1;32m 274\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mload\u001b[39m(fp, \u001b[38;5;241m*\u001b[39m, \u001b[38;5;28mcls\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, object_hook\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, parse_float\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 275\u001b[0m parse_int\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, parse_constant\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, object_pairs_hook\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw):\n\u001b[1;32m 276\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Deserialize ``fp`` (a ``.read()``-supporting file-like object containing\u001b[39;00m\n\u001b[1;32m 277\u001b[0m \u001b[38;5;124;03m a JSON document) to a Python object.\u001b[39;00m\n\u001b[1;32m 278\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 291\u001b[0m \u001b[38;5;124;03m kwarg; otherwise ``JSONDecoder`` is used.\u001b[39;00m\n\u001b[1;32m 292\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 293\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mloads\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 294\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mobject_hook\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mobject_hook\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 295\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_float\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparse_float\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparse_int\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparse_int\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 296\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_constant\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparse_constant\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mobject_pairs_hook\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mobject_pairs_hook\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/py10/lib/python3.10/json/__init__.py:346\u001b[0m, in \u001b[0;36mloads\u001b[0;34m(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)\u001b[0m\n\u001b[1;32m 341\u001b[0m s \u001b[38;5;241m=\u001b[39m s\u001b[38;5;241m.\u001b[39mdecode(detect_encoding(s), \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msurrogatepass\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 343\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\u001b[38;5;28mcls\u001b[39m \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m object_hook \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m\n\u001b[1;32m 344\u001b[0m parse_int \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m parse_float \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m\n\u001b[1;32m 345\u001b[0m parse_constant \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m object_pairs_hook \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kw):\n\u001b[0;32m--> 346\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_default_decoder\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdecode\u001b[49m\u001b[43m(\u001b[49m\u001b[43ms\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 347\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mcls\u001b[39m \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 348\u001b[0m \u001b[38;5;28mcls\u001b[39m \u001b[38;5;241m=\u001b[39m JSONDecoder\n",
"File \u001b[0;32m~/miniconda3/envs/py10/lib/python3.10/json/decoder.py:337\u001b[0m, in \u001b[0;36mJSONDecoder.decode\u001b[0;34m(self, s, _w)\u001b[0m\n\u001b[1;32m 332\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdecode\u001b[39m(\u001b[38;5;28mself\u001b[39m, s, _w\u001b[38;5;241m=\u001b[39mWHITESPACE\u001b[38;5;241m.\u001b[39mmatch):\n\u001b[1;32m 333\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Return the Python representation of ``s`` (a ``str`` instance\u001b[39;00m\n\u001b[1;32m 334\u001b[0m \u001b[38;5;124;03m containing a JSON document).\u001b[39;00m\n\u001b[1;32m 335\u001b[0m \n\u001b[1;32m 336\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 337\u001b[0m obj, end \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mraw_decode\u001b[49m\u001b[43m(\u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43midx\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m_w\u001b[49m\u001b[43m(\u001b[49m\u001b[43ms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mend\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 338\u001b[0m end \u001b[38;5;241m=\u001b[39m _w(s, end)\u001b[38;5;241m.\u001b[39mend()\n\u001b[1;32m 339\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m end \u001b[38;5;241m!=\u001b[39m \u001b[38;5;28mlen\u001b[39m(s):\n",
"File \u001b[0;32m~/miniconda3/envs/py10/lib/python3.10/json/decoder.py:355\u001b[0m, in \u001b[0;36mJSONDecoder.raw_decode\u001b[0;34m(self, s, idx)\u001b[0m\n\u001b[1;32m 353\u001b[0m obj, end \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mscan_once(s, idx)\n\u001b[1;32m 354\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mStopIteration\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n\u001b[0;32m--> 355\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m JSONDecodeError(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mExpecting value\u001b[39m\u001b[38;5;124m\"\u001b[39m, s, err\u001b[38;5;241m.\u001b[39mvalue) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 356\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m obj, end\n",
"\u001b[0;31mJSONDecodeError\u001b[0m: Expecting value: line 1 column 1 (char 0)"
]
}
],
"source": [
"par = {\n",
" 'multiomics_rna': 'resources_test/grn-benchmark/multiomics_rna.h5ad',\n",
" 'tf_all': 'resources_test/prior/tf_all.csv',\n",
" 'prediction': 'output/prediction_scgpt.csv',\n",
" 'max_n_links': 50000,\n",
" 'n_bins': 51,\n",
" 'batch_size': 16,\n",
" 'condition': 'cell_type',\n",
" 'temp_dir': 'output/'\n",
"}\n",
"\n",
"par['model_file'] = f\"{par['temp_dir']}/best_model.pt\"\n",
"par['model_config_file'] = f\"{par['temp_dir']}/args.json\"\n",
"par['vocab_file'] = f\"{par['temp_dir']}/vocab.json\"\n",
"import requests\n",
"def download_file(output_file, url):\n",
" response = requests.get(url, stream=True)\n",
" if response.status_code == 200:\n",
" with open(output_file, \"wb\") as f:\n",
" for chunk in response.iter_content(chunk_size=1024):\n",
" if chunk:\n",
" f.write(chunk)\n",
" print(f\"File downloaded successfully and saved to {output_file}\")\n",
" else:\n",
" print(f\"Failed to download file. HTTP status code: {response.status_code}\")\n",
"# download_file(par['model_file'], 'https://drive.google.com/uc?export=download&id=1CPVtpWUJ2nkI9jGignlHLcefBe6Gk-F9')\n",
"# download_file(par['vocab_file'], 'https://drive.google.com/file/d/1Qzb6Y9UB342a2QxmY-BCubSvcmYZ5jw3/view?usp=drive_link')\n",
"download_file(par['model_config_file'], 'https://drive.google.com/file/d/1VwPGHuSorVAXyTreMFI1yzMougtUDeUt/view?usp=drive_link')\n",
"import json\n",
"with open(par['model_config_file']) as f:\n",
" json.load(f)"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down
2 changes: 1 addition & 1 deletion src/methods/single_omics/scgpt/config.vsh.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ platforms:
image: xueerchen/scgpt:0.1.7
setup:
- type: python
packages: [ ]
packages: [ gdown ]
- type: native
- type: nextflow
directives:
Expand Down
13 changes: 7 additions & 6 deletions src/methods/single_omics/scgpt/script.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,10 @@
import pandas as pd
import tqdm
import os
# import gseapy as gp
# from gears import PertData, GEARS

import requests
import gdown


from scipy.sparse import issparse
import scipy as sp
Expand Down Expand Up @@ -54,7 +56,8 @@
'vocab_file': 'resources_test/supplementary/finetuned_scGPT_adamson/vocab.json',
'n_bins': 51,
'batch_size': 16,
'condition': 'cell_type'
'condition': 'cell_type',
'temp_dir': 'output'
}
## VIASH END
os.makedirs(par['temp_dir'], exist_ok=True)
Expand All @@ -63,8 +66,6 @@
par['model_config_file'] = f"{par['temp_dir']}/args.json"
par['vocab_file'] = f"{par['temp_dir']}/vocab.json"


import requests
def download_file(output_file, url):
response = requests.get(url, stream=True)
if response.status_code == 200:
Expand All @@ -75,11 +76,11 @@ def download_file(output_file, url):
print(f"File downloaded successfully and saved to {output_file}")
else:
print(f"Failed to download file. HTTP status code: {response.status_code}")
download_file(par['model_file'], 'https://drive.google.com/uc?export=download&id=1CPVtpWUJ2nkI9jGignlHLcefBe6Gk-F9')
download_file(par['vocab_file'], 'https://docs.google.com/uc?export=download&id=1Qzb6Y9UB342a2QxmY-BCubSvcmYZ5jw3')
download_file(par['model_config_file'], 'https://docs.google.com/uc?export=download&id=1VwPGHuSorVAXyTreMFI1yzMougtUDeUt')


gdown.download("https://drive.google.com/uc?id=1CPVtpWUJ2nkI9jGignlHLcefBe6Gk-F9", par['model_file'], quiet=False)

# os.environ["PYTORCH_CUDA_ALLOC_CONF"] = "max_split_size_mb:50"
initial_memory = torch.cuda.memory_allocated()
Expand Down

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