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        def RunModule(infile_name):
    #Run the necessary module functions
    contigs = cafParse(infile_name)
    variation = FindSNPs(contigs)
    TCSwriter(infile_name, variation)
        


src/4/p/4Pipe4-HEAD/4Pipe4.py   4Pipe4(Download)
def DiscoveryTCS(basefile):
    #Discovers SNPs in the TCS output file of Mira. Use only if trying to find SNPs. Output in TCS format.
    os.chdir(os.path.split(basefile)[0])
    print("\nRunning SNP Discovery tool module...")
    CAF_to_TCS.RunModule(basefile + '_assembly/' + miraproject + '_d_results/' + miraproject + '_out.caf')