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


    

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using Kraft: count_transcript


    

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for (sample_name, fastq_file_paths) in
    zip(PROJECT_JSON["sample_names"], PROJECT_JSON["fastq_file_paths"])

    count_transcript(
        abspath.(fastq_file_paths)...,
        abspath(PROJECT_JSON["reference_cdna_fasta_file_path"]),
        joinpath(PATH["count_transcript/"], sample_name),
        PROJECT_JSON["n_job"],
    )

end