Exemplo n.º 1
0
def loadargs():
    global datadir
    args = argparse.ArgumentParser(
        description="Generate the HT-SELEX experiments.")
    args.add_argument(
        "--jolma",
        action="store_true",
        default=False,
        help=
        "Use this flag to train on the HT-SELEX cycles selected by Jolma et al., rather than the cycles selected by Alipanahi et al."
    )
    args = util.parseargs("selex", args)
    if args.jolma:
        args.calibdir = args.outdir + "/jolma/calib"
        args.finaldir = args.outdir + "/jolma/final"
        args.reportdir = args.outdir + "/jolma/report"
        args.testdir = args.outdir + "/jolma/test"
        datadir = datadir + "/jolma"
    else:
        args.calibdir = args.outdir + "/best/calib"
        args.finaldir = args.outdir + "/best/final"
        args.reportdir = args.outdir + "/best/report"
        args.testdir = args.outdir + "/best/test"
        datadir = datadir + "/best"
    return args
def loadargs():
    args = argparse.ArgumentParser(description="Generate the ENCODE experiments.")
    args.add_argument("mode", type=str, help="Either \"top\" (train top 500 odd, test top 500 even) or \"all\" (train top 500 even + all after 1000, test top 500 even).")
    args = util.parseargs("encode", args)
    args.calibdir  = args.calibdir.replace(args.outdir, args.outdir+"/"+args.mode)
    args.finaldir  = args.finaldir.replace(args.outdir, args.outdir+"/"+args.mode)
    args.reportdir = args.reportdir.replace(args.outdir,args.outdir+"/"+args.mode)
    args.outdir    = args.outdir+"/"+args.mode
    return args
Exemplo n.º 3
0
def loadargs():
    args = argparse.ArgumentParser(
        description="Generate the ENCODE experiments.")
    args.add_argument(
        "mode",
        type=str,
        help=
        "Either \"top\" (train top 500 odd, test top 500 even) or \"all\" (train top 500 even + all after 1000, test top 500 even)."
    )
    args = util.parseargs("encode", args)
    args.calibdir = args.calibdir.replace(args.outdir,
                                          args.outdir + "/" + args.mode)
    args.finaldir = args.finaldir.replace(args.outdir,
                                          args.outdir + "/" + args.mode)
    args.reportdir = args.reportdir.replace(args.outdir,
                                            args.outdir + "/" + args.mode)
    args.outdir = args.outdir + "/" + args.mode
    return args
Exemplo n.º 4
0
def loadargs():
    global datadir
    args = argparse.ArgumentParser(description="Generate the HT-SELEX experiments.")
    args.add_argument("--jolma", action="store_true", default=False, help="Use this flag to train on the HT-SELEX cycles selected by Jolma et al., rather than the cycles selected by Alipanahi et al.")
    args = util.parseargs("selex", args)
    if args.jolma:
        args.calibdir  = args.outdir+"/jolma/calib"
        args.finaldir  = args.outdir+"/jolma/final"
        args.reportdir = args.outdir+"/jolma/report"
        args.testdir   = args.outdir+"/jolma/test"
        datadir = datadir + "/jolma"
    else:
        args.calibdir  = args.outdir+"/best/calib"
        args.finaldir  = args.outdir+"/best/final"
        args.reportdir = args.outdir+"/best/report"
        args.testdir   = args.outdir+"/best/test"
        datadir = datadir + "/best"
    return args
Exemplo n.º 5
0
def loadargs():
    # Give names to specific groups of RNAcompete ids
    args = argparse.ArgumentParser(
        description="Generate the RNAcompete experiments.")
    args.add_argument(
        "mode",
        type=str,
        help=
        "Either \"A\" (train A, test B), \"B\" (train B, test A), or \"AB\" (train AB, test invivo)."
    )
    args = util.parseargs("rnac", args, shorthandids=shorthandids)
    args.calibdir = args.calibdir.replace(args.outdir,
                                          args.outdir + "/" + args.mode)
    args.finaldir = args.finaldir.replace(args.outdir,
                                          args.outdir + "/" + args.mode)
    args.reportdir = args.reportdir.replace(args.outdir,
                                            args.outdir + "/" + args.mode)
    args.outdir = args.outdir + "/" + args.mode
    return args
Exemplo n.º 6
0
def loadargs():
    args = argparse.ArgumentParser(description="Generate the DREAM5 PBM and/or CHIP experiments.")
    args = util.parseargs("dream5", args)
    return args
Exemplo n.º 7
0
def loadargs():
    args = argparse.ArgumentParser(
        description="Generate the DREAM5 PBM and/or CHIP experiments.")
    args = util.parseargs("dream5", args)
    return args