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
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
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():
# 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
def loadargs():
args = argparse.ArgumentParser(description="Generate the DREAM5 PBM and/or CHIP experiments.")
args = util.parseargs("dream5", args)
return args
def loadargs():
args = argparse.ArgumentParser(
description="Generate the DREAM5 PBM and/or CHIP experiments.")
args = util.parseargs("dream5", args)
return args