https://github.com/KoslickiLab/WGSUniFrac
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Tip revision: 02e1849f4a611b8623bd449dbc8178ef785e68a9 authored by Wei Wei on 15 June 2022, 19:04:10 UTC
remove more unneeded files
Tip revision: 02e1849
get_wgs_pcoa_plot.py
import taxunifrac as tu
import argparse

def main():
    parser = argparse.ArgumentParser(description="Get pcoa plot of taxonomic profiles in a direcory.")
    parser.add_argument('-dir', '--dir', type=str, help="The directory where profiles are located.")
    parser.add_argument('-t', '--plt_title', type=str, help="Title of the pcoa plot.")
    parser.add_argument('-a', '--alpha', type=float, help="The factor for branch length function. -1, -0.5, 0, 1, 5")

    args = parser.parse_args()
    dir = args.dir
    plt_title = args.plt_title
    alpha = args.alpha

    #sample_lst, dist_matrix, metadata = tu.pairwise_unifrac(dir, plt_title)
    tu.pairwise_unifrac(dir, plt_title, alpha)

if __name__ == "__main__":
    main()
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