Instalation

macOS/Linux

To instal ExtraARGs algorighm just follow this instructions:

    git clone https://github.com/gaarangoa/ExtrARG.git
    cd ./ExtrARG/src/
    pip install .

Check the instalation by typing:

    extrarg -h

Run a test:

    extrarg --input-file ../test/PIRE_INFLUENT.xlsx --output-file ../test/temp

Windows

Requirements

    python 2.7 or python 3.x
    git (https://git-scm.com/download/win)
    pip (https://pip.pypa.io/en/stable/installing/)

Instalation

    git clone https://github.com/gaarangoa/ExtrARG.git
    cd ./ExtrARG/src/
    python -m pip install .

Check the instalation by typing:

    extrarg -h

Run a test

    python -m extrarg --input-file ../test/PIRE_INFLUENT.xlsx --output-file ../test/temp

Usage

Before using ExtrARG, please make sure the format of your input contains the required fields.

    extrarg --help # (macOS/linux)
    python -m extrarg --help # (Windows)
    Usage: extrarg [OPTIONS]

    This program subtract the top N (50 default) discriminatory antibiotic
    resistance genes from a set of metagenomics samples. Hyperparameters of
    the supervised machine learning algorithm (extra tree classifier) are
    automatically tuned using the bayesian optimization.

    Options:
    --input-file TEXT       input excel file
    --output-file TEXT      output file where to store the results
    --min-reads INTEGER     minimum number of reads on each ARG (default 1)
    --epochs INTEGER        number of iterations the optimization algorithm run
                            (default 50)
    --max-importance FLOAT  maximum importance for search space (default 0.01)
    --min-importance FLOAT  minimum importance for search space (default 1e-5)
    -h, --help              Show this message and exit.