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Mycorrhiza population assignment tools.

Project description

Mycorrhiza

Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data.

Installing Mycorrhiza with pip

  1. Make sure you have the latest version of Python 3.x

    python --version
    
  2. Install pip

    python -m pip install --upgrade pip setuptools wheel
    
  3. Install Mycorrhiza

    pip install --upgrade mycorrhiza
    
  4. Install SplitsTree

    Installation executables for SplitsTree4 can be found here.

  5. Install Matplotlib

    Instructions can be found here.

Running an analysis

  1. Import the necessary modules.

    from mycorrhiza.dataset import Myco
    from mycorrhiza.analysis import CrossValidate
    from mycorrhiza.plotting.plotting import mixture_plot
    
  2. (Optional) By default Mycorrhiza will look for SplitStree in your PATH. I you wish to specify a different path for the SplitsTree executable you can do so in the settings module.

    from mycorrhiza.settings import const
    const['__SPLITSTREE_PATH__'] = 'SplitsTree'
    
  3. Load some data. Here data is loaded in the Mycorrhiza format from the Gipsy moth sample data file. Example data can be found here.

    myco = Myco(file_path='data/gipsy.myc')
    myco.load()
    
  4. Run an analysis. Here a simple 5-fold cross-validation analysis is executed on all available loci, without partitioning.

    cv = CrossValidate(dataset=myco, out_path='data/')
    cv.run(n_partitions=1, n_loci=0, n_splits=5, n_estimators=60, n_cores=1)
    
  5. Plot the results.

    mixture_plot(cv)
    

Documentation

https://jgeofil.github.io/mycorrhiza/

File formats

Myco

Diploid genotypes occupy 2 rows (the sample identifier must be identical).

Column(s) Content Type
1 Sample identifier string
2 Population string or integer
3 Learning flag {0,1}
4 to M+3 Loci {A, T, G, C, N}

STRUCTURE

Diploid genotypes occupy 2 rows (the sample identifier must be identical).

Column(s) Content Type
1 Sample identifier string
2 Population integer
3 Learning flag {0,1}
4 to O+3 Optional (Ignored)
O+3 to M+O+3 Loci integer or -9

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