engreitzlab / encode_re2g Goto Github PK

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

• config_biosamples.txt
• error_message.pdf
• write_powerlaw_params [workaround].txt