cMatch

Prerequisite

You need Python 3.9 and pip the package installer for Python pip

Install

Install a virtual environment if you want.

    $ python3 -m venv --prompt cmatch venv
    $ source ./venv/bin/activate

Install teh dependencies

    $ pip install -r requirements.txt

cMatch command line tool

run cmatch.py

    $ ./cmatch.py --help 

Simple Example

Run cMatch on a simple example, matching the violacein template (template.json) and two synthetic violacein constructs (vio-B0030-B0030-B0030-B0030-B0030.seq, vio-B0030-B0031-B0032-B0033-B0064.seq).

    $ cd simple_example/
    $ ../cmatch.py template.json vio-B0030-B0030-B0030-B0030-B0030.seq vio-B0030-B0031-B0032-B0033-B0064.seq

The cmatch tool will output JSON.

Run the tests

Run the tests for algorithm CM_0

    $ python Testing_Algorithm_CM_0.py

Run the tests for algorithm CM_1

    $ python Testing_Algorithm_CM_1.py

Run the tests for algorithm CM_2 First Example

    $ python test_cm2_vio_easy_1vs1_th75.py
    $ python test_cm2_vio_easy_1vs1_th99.py
    $ python test_cm2_vio_hard_1vs1_th75.py
    $ python test_cm2_vio_hard_1vs1_th99.py

Run the tests for algorithm CM_2 Second Example

    $ python test_cm2_vio_easy_1vsAll_th75.py
    $ python test_cm2_vio_easy_1vsAll1_th99.py
    $ python test_cm2_vio_hard_1vsAll1_th75.py
    $ python test_cm2_vio_hard_1vsAll1_th99.py

Run the tests for algorithm CM_2 Real life example Lycopene Operon

    $ python test_cm2_lycopene_sanger_10.py
    $ python test_cm2_lycopene_sanger_100.py

Run the tests for algorithms CM_1, CM_2 Violacein-0000 cat x2 and cat x3

    $ python cm1_cat2.py
    $ python cm1_cat2min.py

    $ python cm1_cat3.py
    $ python cm1_cat3min.py

    $ python cm2_cat2.py
    $ python cm2_cat2min.py

    $ python cm2_cat3.py
    $ python cm2_cat3min.py