def init_argparser(p=None):
p = naltparser.init_argparser(p)
p.add_argument('-o', '--outfile')
p.add_argument('--type', default='nalt', choices=['nalt', 'ralt'])
return p
def init_argparser(p=None):
p = naltparser.init_argparser()
p.add_argument('--countmissing', default=False, action='store_true')
p.add_argument('-o', '--outfile', default='outfile.dist.txt')
p.add_argument('--includepos', default=None)
return p
def init_argparser(p=None):
p = naltparser.init_argparser(with_group=False)
p.add_argument('--includepos', default='')
p.add_argument('--revfmt', default=False, action='store_true')
p.add_argument('-o', '--outfile', default='outfile.haplotypes.txt')
return p
def init_argparser(p=None):
if not p:
p = arg_parser("ralt2allqc - checking exhaustively")
p = naltparser.init_argparser(p, with_group=False, with_position=False)
p.add_argument('--mac', type=int, default=1, help="Minor Allele Count")
p.add_argument('--miss', type=float, default=1.0, help='Missingness fraction threshold')
p.add_argument('-k', type=int, default=-1, help='start from individual/samples no K')
p.add_argument('-o', '--outfile', default='out.exhqc.txt')
p.add_argument('-s', type=int, default=-1, help='no of sample to be exported')
return p
def init_argparser(p=None):
if p is None:
p = arg_parser('classify.py - classify samples based on SNP barcodes')
p = naltparser.init_argparser(p)
p.add_argument('--profile', default=None, required=True)
p.add_argument('--includepos', default=None, required=True)
p.add_argument('--code', default=None, required=True)
p.add_argument('--remark', default=None, required=True)
p.add_argument('--replace', default=False, action='store_true')
p.add_argument('--update', default=False, action='store_true')
return p
def init_argparser():
parser = arg_parser("simxval.py - simulate cross-validation of likelihood evaluator with various model and k")
parser.add_argument('-m', '--method', help ='method to use : list rand dt hfst hhfstdt')
parser.add_argument('-k', default='100,50', help='k list')
parser.add_argument('--iter', default=5, type=int, help='iteration per fold')
parser.add_argument('--repeats', default=20, type=int, help='n repeats of fold')
parser.add_argument('--fold', default=10, type=int)
parser.add_argument('--mac', default=0, type=int)
parser.add_argument('-o', '--outfile', default='out.accuracy.dt.txt')
parser.add_argument('--outsnp', default=None)
parser.add_argument('--snpfile', default=None, help='file containing list of SNPs for list method')
parser.add_argument('-j', default=1, type=int, help='No of process')
parser.add_argument('--guidetree', default=None)
parser.add_argument('--minfst', type=float, default=0.9, help='min FST for hfst method')
parser.add_argument('--logfile', default=None, help='log file output')
parser = naltparser.init_argparser(parser)
return parser
def init_argparser(p=None):
if not p:
p = arg_parser("ralt2allqc - checking exhaustively")
p = naltparser.init_argparser(p)
p.add_argument('--indvindex', default=None)
p.add_argument('--posindex', default=None)
p.add_argument('--includepos', default=None)
p.add_argument('--excludesample', default=None)
p.add_argument('--includesample', default=None)
p.add_argument('--completesamples', default=False, action="store_true")
p.add_argument('--mac', default=0, type=int)
p.add_argument('--type', default='ralt')
p.add_argument('--autofilename', default=False, action='store_true')
p.add_argument('--outfmt', default='text', choices=['text', 'pickle', 'npy'])
p.add_argument('-o', '--outfile', default='outfile')
return p
def init_argparser():
p = arg_parser("Convert r_alt datafile to n_alt datafile")
p.add_argument('-o', '--outfile', default='outdata')
p.add_argument('-r',
'--hetratio',
type=float,
default=0.25,
help="ratio for calling heterozygosity")
p.add_argument('-m',
'--major',
action="store_true",
help="set all caling to major allele")
p.add_argument('--missingtohet',
action='store_true',
help="set missing as heterozygosity")
p.add_argument('--outfmt', default='npy', choices=['npy', 'pickle', 'tab'])
p.add_argument('--autofilename', default=True, action='store_true')
# option to treat all missing as hets
p = naltparser.init_argparser(p, with_group=False, with_position=False)
return p
def init_argparser(p = None):
if p is None:
p = arg_parser('lkest.py - SNP-based likelihood estimator')
p = naltparser.init_argparser(p)
p.add_argument('-c', '--config', default=None, help = 'config file to use (optional)')
p.add_argument('--mode', default='predict', choices = mode.keys()
, help = 'run mode')
p.add_argument('--logfile', default=None)
p.add_argument('-o', '--outfile', default='outfile.txt')
# cross validation params
p.add_argument('--repeats', default=10, type=int, help='number of repeats')
p.add_argument('--fold', default=5, type=int, help='number of fold')
p.add_argument('--iter', default=1, type=int, help='iteration per fold')
# simulate
p.add_argument('-j', default=1, type=int, help='no of process')
p.add_argument('--outsnp', default=None, help='output filename for index of SNPs')
p.add_argument('-m', '--method', choices=['fix', 'rand', 'list', 'dt', 'hfst', 'hfst+dt'])
p.add_argument('-k', default='100,50'
, help='list of k, with k interpreted depending on selected method')
p.add_argument('--insnp', default=None, help='input file containing index of SNPs')
p.add_argument('--guidetree', default=None, help='guide tree used by hfst and hfst+dt')
p.add_argument('--minfst', default=None, help='minimum FST for hfst and hfst+dt')
p.add_argument('--mac', default=0, help='filtering for MAC')
# train
p.add_argument('--outprofile')
# predict
p.add_argument('--inprofile')
return p
def init_argparser():
parser = arg_parser('Assess SNP and sample quality from nalt file')
parser = naltparser.init_argparser(parser, with_group=False)
return parser