Usage

Command-line Interface

oddSNP exposes several CLI commands grouped by submodule.

cpSNP-IC

Run the full cpSNP-IC pipeline:

python -m oddSNP cpsnpic run-all <INPATH> <OUPATH>

Run individual steps:

python -m oddSNP cpsnpic calculate-cpsnpic <INPATH> <OUPATH>
python -m oddSNP cpsnpic generate-histogram <CPFILE> <OUPATH>
python -m oddSNP cpsnpic save-cpsnpic-plot <HISTOFILE> <OUTPUT>

SNP-IC

python -m oddSNP snpic [OPTIONS] COMMAND [ARGS]...

Python API

You can also call oddSNP functions directly from Python:

from oddSNP import cpsnpic

cpsnpic.call_run_all(
    inpath='path/to/pileup/',
    oupath='path/to/output/',
    nproc=20,
    batch_size=100000,
    force=False
)