import pydeseq2
from pydeseq2.utils import load_example_data
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats

print(f'version == {pydeseq2.__version__}')
counts_df = load_example_data(
    modality="raw_counts",
    dataset="synthetic",
    debug=False,
)

metadata = load_example_data(
    modality="metadata",
    dataset="synthetic",
    debug=False,
)
metadata=metadata.loc[[f'sample{i}' for i in [*range(1,11),*range(91,101)]]]
counts_df=counts_df.loc[metadata.index]

counts_df.loc[:,'geneX']=0
counts_df.loc['sample100','geneX']=100

dds = DeseqDataSet(
    counts=counts_df,
    metadata=metadata,
    design_factors="condition",
    refit_cooks=True,
)
dds.deseq2()

stat_res = DeseqStats(dds)
stat_res.summary()