diffsplice_fishers_exact error: cannot import name 'main' from 'flair.diffsplice_fishers_exact'

[ZDD116]

Hi Flair team,

I'm using diffsplice_fishers_exact to analyze my data without replicates. The pipeline seems finished, and I have all documents generated, but there is an error message as follows.

Could you please confirm what the problem is? Is my output affected by the error, and should I not trust the results? Thank you.

Copy and paste the exact command you tried to run
source /home/ZDD/.bashrc
conda activate flair3

cd $PBS_O_WORKDIR/flair3
mkdir -p diffsplice_fishers

CONDA_SITE_PACKAGES=$(python -c "import site; print(site.getsitepackages()[0])")

export PYTHONPATH="${CONDA_SITE_PACKAGES}:${PYTHONPATH}"

echo "Subprocesses will now use site-packages from: $PYTHONPATH"
python -c "import pysam; print('Pysam path verified:', pysam.file)"

export PYTHONPATH=$CONDA_PREFIX/lib/python3.12/site-packages:$PYTHONPATH

for as in alt5 alt3 es ir; do
while read ebv_pos; do
/home/manzhai/miniconda3/envs/flair3/bin/diffsplice_fishers_exact
diffSplice/diffsplice.${as}.events.quant.tsv
NP361_condition1_batch2
${ebv_pos}_condition2_batch2
diffsplice_fishers/${as}NP361${ebv_pos}.fishers.tsv
done < "../ebv_pos.list"
done

How did you install Flair?
bioconda (e.g. conda create -n flair -c conda-forge -c bioconda flair)

Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)
Traceback (most recent call last):
  File "/home/ZDD/miniconda3/envs/flair3/bin/diffsplice_fishers_exact", line 3, in <module>
    from flair.diffsplice_fishers_exact import main
ImportError: cannot import name 'main' from 'flair.diffsplice_fishers_exact' (/home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py)

[diekhans]

I see why this is happening for you. The flair/diffsplice_fishers_exact.py doesn't have a main() function. It is just an inline script.

pip install create a program to call the main in the library.

However, I am mystified. This doesn't fail in my test cases. Somehow the Python startup determines there isn't a main and just runs the program. I need to understand why.

Meanwhile, you can run the program with:

python3 /home/ZDD/miniconda3/envs/flair3/lib/python3.12/site-packages/flair/diffsplice_fishers_exact.py

[diekhans]

This is fixed in the master branch and will go out in the next releaase