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using JSON: parse


    

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PROJECT_JSON = parse(read("../project.json", String))


    

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using PyCall: @py_str, pyimport


    

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py"""
import sys

sys.path.insert(0, ".")
"""

PATH = pyimport("make_path_dict").make_path_dict(PROJECT_JSON)


    

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using CSV


    

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const gene_x_sample = CSV.read(PATH["gene_x_sample.processed.tsv"])


    

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push!(LOAD_PATH, "/home/kwat/github/Kraft.jl/src")


    

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using Kraft: read_gmt


    

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const gene_set_name_genes = read_gmt(String.(PROJECT_JSON["gene_set_file_paths"]))

const gene_set_x_information = CSV.read(PATH["gene_set_x_information.tsv"])

for i = 1:size(gene_set_x_information, 1)
    if gene_set_x_information[i, Symbol("Good")] == 0

        delete!(gene_set_name_genes, gene_set_x_information[i, Symbol("Gene Set")])

    end

end


    

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using Kraft: make_gene_set_x_sample


    

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gene_set_x_sample = make_gene_set_x_sample(
    gene_x_sample,
    gene_set_name_genes;
    gene_set_x_sample_file_path = PATH["gene_set_x_sample.tsv"],
)