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# ---
# jupyter:
# jupytext:
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# extension: .py
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# ---
# %%
# If not done before: combine adatas!
from pathlib import Path
import pandas as pd
import scanpy as sc
from chemCPA.paths import PROJECT_DIR
adatas = [
sc.read(PROJECT_DIR / "datasets" / f"adata_{split}_biolord_split_30.h5ad") for split in ["train", "test", "ood"]
]
# adatas = [sc.read(Path("project_folder") / "datasets" / f"adata_{split}_biolord_split_30.h5ad") for split in ["train", "test"]]
for adata in adatas:
df = adata.obs
for col in df.select_dtypes(["category"]).columns:
_type = type(df[col].cat.categories[0])
print(f"{col}: {_type}")
try:
df[col] = df[col].astype(_type)
except:
print(col)
df[col] = df[col].astype(str)
adata = sc.concat(adatas)
key_check = (
~pd.Series(adatas[0].uns["rank_genes_groups_cov_all"].keys()).isin(
list(adatas[1].uns["rank_genes_groups_cov_all"].keys())
)
).sum()
print(f"Key check: {key_check} should be 0.")
adata.uns["rank_genes_groups_cov_all"] = adatas[0].uns["rank_genes_groups_cov_all"]
# Add proper DMSO
adata.obs["smiles"].replace("nan", "CS(C)=O", inplace=True)
# %%
sc.write(Path("project_folder") / "datasets" / "adata_biolord_split_30.h5ad", adata)
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