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View Code? Open in Web Editor NEWEnhancer-Gene Prediction Pipeline based on logistic regression and ABC model
Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model
When running the snakemake workflow, on K562 Chr22 example, I get this error
python: can't open file '/home/oweyi/week_2/issue/encode_e2g_features/workflow/scripts/compute_powerlaw_fit_from_hic.py': [Errno 2] No such file or directory
.
This occurs when my config_biosamples.tsv
row contains HiC_dir
, HiC_type
, HiC_resolution
but not HiC_gamma
nor HiC_scale
. My intention is that config should invoke compute_powerlaw_fit_from_hic.py to calculate, for the first run, the HiC parameters using the juicebox HiC folder.
This particular configuration triggers write_powerlaw_params.smk
to run this shell command
python ABC/workflow/scripts/write_powerlaw_params.py --hic_dir ABC/example_chr/HiC_K562 --hic_type juicebox --hic_resolution 5000 --output_file results/HiC_Powerlaw/fade7e41/hic.powerlaw.tsv
.
Since HiC_gamma
and HiC_scale
are not provided, the script runs write_powerlaw_params.py > exec_compute_powerlaw_fit_script
.
This function tries to run the python script compute_powerlaw_fit_from_hic.py
from the encode_e2g_features/workflow/scripts
folder rather than the correct encode_e2g_features/ABC/workflow/scripts
folder.
The current workaround I'm using is to shove in the correct path in the write_powerlaw_params.py > exec_compute_powerlaw_fit_script
function with __file__
dunder variable under the assumption that write_powerlaw_params.py
and compute_powerlaw_fit_from_hic.py
will be in the same folder.
Attached is the
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