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Update perturb_dataset.py #48

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24 changes: 15 additions & 9 deletions src/data/perturb_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,19 +95,25 @@ def __init__(self, adata, data_path, spectral_parameter, spectra_params, fm, sta
self.all_perts_test = pkl.load(f)

if self.data_name == "replogle_rpe1":
if not os.path.exists(f"{self.data_path}/input_features/train_data_{self.spectral_parameter}.pkl.gz"):
ctrl_adata, pert_adata, train, test, pert_list = self.preprocess_and_featurise(adata)
pp_data = self.featurise_replogle(pert_adata, pert_list, ctrl_adata, train, test)
self.X_train, self.train_target, self.X_val, self.val_target, self.X_test, self.test_target = pp_data
if not os.path.exists(f"{feature_path}/train_data_{self.spectral_parameter}.pkl.gz"):
(self.X_train, self.train_target, self.X_val, self.val_target, self.X_test, self.test_target,
self.ctrl_expr, _) = self.preprocess_and_featurise(adata)
else:
with gzip.open(f"{self.data_path}/input_features/train_data_{self.spectral_parameter}.pkl.gz",
"rb") as f:
self.basal_ctrl_adata = sc.read_h5ad(
f"{self.data_path}/basal_ctrl_{self.data_name}_pp_filtered.h5ad")
with gzip.open(f"{feature_path}/train_data_{self.spectral_parameter}.pkl.gz", "rb") as f:
self.X_train, self.train_target = pkl.load(f)
with gzip.open(f"{self.data_path}/input_features/val_data_{self.spectral_parameter}.pkl.gz", "rb") as f:
with gzip.open(f"{feature_path}/val_data_{self.spectral_parameter}.pkl.gz", "rb") as f:
self.X_val, self.val_target = pkl.load(f)
with gzip.open(f"{self.data_path}/input_features/test_data_{self.spectral_parameter}.pkl.gz",
"rb") as f:
with gzip.open(f"{feature_path}/test_data_{self.spectral_parameter}.pkl.gz", "rb") as f:
self.X_test, self.test_target = pkl.load(f)
if PerturbData.ctrl_expr_cache is None:
with open(f"{self.data_path}/raw_expression_{self.data_name}_pp_filtered.pkl", "rb") as f:
PerturbData.ctrl_expr_cache = pkl.load(f)
self.ctrl_expr = PerturbData.ctrl_expr_cache
else:
with open(f"{self.data_path}/raw_expression_{self.data_name}_pp_filtered.pkl", "rb") as f:
self.ctrl_expr = pkl.load(f)

if self.data_name == "replogle_k562":
if not os.path.exists(f"{feature_path}/train_data_{self.spectral_parameter}.pkl.gz"):
Expand Down