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Feature/no ref/foundation model #449

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KaiWaldrant committed Apr 29, 2024
commit 4abf355aa4ffe1e8066b1b188fc19912a7c12f11
25 changes: 25 additions & 0 deletions src/tasks/batch_integration/methods/scgpt/script.py
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import numpy as np
import anndata as ad
import json
from scgpt.tokenizer.gene_tokenizer import GeneVocab
from scgpt.model import TransformerModel
from scgpt.utils.util import load_pretrained
import torch

## VIASH START

par = {
'input': 'resources_test/batch_integration/pancreas/dataset.h5ad',
'model': 'resources_test/batch_integration/scgpt/pretrained_model',
'model_config': 'resources_test/batch_integration/scgpt/pretrained_model/config.json',
'model_vocab': 'resources_test/batch_integration/scgpt/pretrained_model/vocab.json',
'output': 'output.h5ad'
}

meta = {
'functionality_name' : 'scgpt',
}

## VIASH END


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