PyDESeq2
PyDESeq2 copied to clipboard
[BUG] DeseqDataSet.deseq2() still prints when quiet=True is set
Describe the bug
My following code
from pydeseq2.dds import DeseqDataSet
from pydeseq2.default_inference import DefaultInference
inference = DefaultInference(n_cpus=1)
dds = DeseqDataSet(counts=..., metadata=..., design_factors=..., inference=inference, quiet=True)
dds.deseq2()
still prints the following 3 sentences when quiet=True
, while from the source code they should be controlled by quiet
parameter:
Fitting dispersions...
... done in 0.20 seconds.
Fitting MAP dispersions...
... done in 0.22 seconds.
Fitting LFCs...
... done in 0.17 seconds.
To Reproduce
This case happens for some data, not all. However, my case uses internal data, so I may have to do some anonymization work before sharing it with you.
Expected behavior
These sentences should not be printed if quiet=True
is set.
Screenshots
Already shown above.
Desktop (please complete the following information):
- OS: Ubuntu 22.04.4 LTS
- Version: pydeseq2 v0.4.9
Additional context Add any other context about the problem here.