def read_params(args):
parser = argparse.ArgumentParser(description='''beta cluster wrapper | v1.0 at 2015/10/16 by liangzb ''')
parser.add_argument('--jackknifed_beta_diversity', dest='jack_soft', metavar='STR', type=str,
default="jackknifed_beta_diversity.py",
help="set the jackknifed_beta_diversity.py, default find in env")
parser.add_argument('--make_bootstrapped_tree', dest='bootstrap_soft', metavar='STR', type=str,
default="make_bootstrapped_tree.py",
help="set the make_bootstrapped_tree.py, default find in env")
parser.add_argument('-i', '--otu_biom', dest='otu_biom', metavar='FILE', type=str, required=True,
help="set the otu biom file")
parser.add_argument('-t', '--tree_file', dest='tree_file', metavar='FILE', type=str, required=True,
help="set the tree file")
parser.add_argument('-g', '--group_file', dest='group_file', metavar='FILE', type=str, default=None,
help="set the group file")
parser.add_argument('-s', '--seqs_per_sample', dest='seqs', metavar="INT", type=int, default=None,
help="set the seqs_per_sample, can be overrited if set stat_file")
parser.add_argument('--stat_file', dest='stat_file', metavar='FILE', type=str, default=None,
help="set the stat file produced by 01_stat.py")
parser.add_argument('--add_params', dest='add_params', metavar='STR', type=str, default=None,
help="add params commands")
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='DIR', type=str, required=True,
help="set the output dir")
args = parser.parse_args()
params = vars(args)
if params['stat_file'] is not None:
maximum, minimum = parse_stat_file(params['stat_file'], group_file=params['group_file'])
params['seqs'] = minimum
if params['group_file'] is not None:
params['group'] = parse_group_file(params['group_file'])
if params['seqs'] is None and params['stat_file'] is None:
parser.print_help()
sys.exit()
return params
def read_params(args):
parser = argparse.ArgumentParser(description='''downsize script | v1.0 at 2015/09/28 by liangzb ''')
parser.add_argument('-m', '--minimum', dest='minimum', metavar='INT', type=int, default=None,
help="set the minimum to downsize, [default is None]")
parser.add_argument('-s', '--in_statfile', dest='statfile', metavar='INT', type=str, default=None,
help="find the minimum from statfile which produced by 01_stat, can be overrited by MINIMUM")
parser.add_argument('-i', '--otu_mapfile', dest='otu_map', metavar='STR', type=str, required=True,
help="set the otu_mapfile")
parser.add_argument('-o', '--outfile', dest='outfile', metavar='OUTFILE', type=str, required=True,
help="set the output file")
parser.add_argument('--out_statfile', dest='outstatfile', metavar='FILE', type=str, default=None,
help="set the stat file")
parser.add_argument('--keep_small_size', dest='keep', action='store_true',
help="keep the small size [default]")
parser.add_argument('--no_keep_small_size', dest='keep', action='store_false',
help="do not keep the small size")
parser.set_defaults(keep=True)
parser.add_argument('--random', dest='random', action='store_true',
help="downsize random [default]")
parser.add_argument('--no_random', dest='random', action='store_false',
help="do not downsize random")
parser.set_defaults(random=True)
parser.add_argument('-g', '--group', dest='group', metavar='FILE', type=str, default=None,
help="if set the group file, in_stat_file will be overwrited")
args = parser.parse_args()
params = vars(args)
if params['minimum'] is None and params['statfile'] is None:
parser.print_help()
sys.exit()
if params['minimum'] is None and params['statfile'] is not None:
maximum, params['minimum'] = parse_stat_file(params['statfile'], group_file=params['group'])
params['group'] = parse_group_file(params['group'])
return params
def read_params(args):
parser = argparse.ArgumentParser(description='multiple_rarefactions | v1.0 at 2015/09/21 by liangzb')
parser.add_argument('-r', '--multiple_rarefactions', dest='multiple_rarefactions', metavar='STR',
default='multiple_rarefactions.py',
help="set the path of multiple_rarefactions.py, default will find in PATH")
parser.add_argument('-i', '--infile', dest='infile', metavar='FILE', type=str, required=True,
help="set the input biom file")
parser.add_argument('-o', '--outdir', dest='outdir', metavar='OUTDIR', type=str, default='./rarefaction',
help="set the output dir, [default is PWD/rarefaction ]")
parser.add_argument('-m', '--min', dest='min', metavar='INT', type=int, default=10,
help="minimum of seqs for rarefaction, [default is 10]")
parser.add_argument('-s', '--step', dest='step', metavar='INT', type=int, default=4000,
help="size of steps between min/max, [default is 4000]")
parser.add_argument('-c', '--choice_mode', dest='mode', metavar='STR', choices=['MIN', 'MAX'], default='MAX',
help="set the stat pick method, MIN or MAX, [default is 'MAX']")
parser.add_argument('-x', '--max', dest='max', metavar='INT', type=int,
help="maximum of seqs for rarefaction, make sure that at least one sample's seq num "
"must over this number it can be overrited by STATFILE")
parser.add_argument('-t', '--statfile', dest='statfile', metavar='FILE', type=str, default=None,
help="set the statfile produced by 01_stat.py")
parser.add_argument('-g', '--group', dest='group_file', metavar='FILE', type=str, default=None,
help="set the group_file ")
args = parser.parse_args()
params = vars(args)
if params['statfile'] is not None:
maximum, minimum = parse_stat_file(params['statfile'], group_file=params['group_file'])
print "maximum is :%s" % maximum
print "minimum is : %s" % minimum
if params['mode'] == 'MAX':
params['max'] = maximum
elif params['mode'] == 'MIN':
params['max'] = minimum
if params['max'] is None and params['statfile'] is None:
parser.print_help()
sys.exit()
return params
def read_params(args):
parser = argparse.ArgumentParser(
description='multiple_rarefactions | v1.0 at 2015/09/21 by liangzb')
parser.add_argument(
'-r',
'--multiple_rarefactions',
dest='multiple_rarefactions',
metavar='STR',
default='multiple_rarefactions.py',
help=
"set the path of multiple_rarefactions.py, default will find in PATH")
parser.add_argument('-i',
'--infile',
dest='infile',
metavar='FILE',
type=str,
required=True,
help="set the input biom file")
parser.add_argument(
'-o',
'--outdir',
dest='outdir',
metavar='OUTDIR',
type=str,
default='./rarefaction',
help="set the output dir, [default is PWD/rarefaction ]")
parser.add_argument(
'-m',
'--min',
dest='min',
metavar='INT',
type=int,
default=10,
help="minimum of seqs for rarefaction, [default is 10]")
parser.add_argument(
'-s',
'--step',
dest='step',
metavar='INT',
type=int,
default=4000,
help="size of steps between min/max, [default is 4000]")
parser.add_argument(
'-c',
'--choice_mode',
dest='mode',
metavar='STR',
choices=['MIN', 'MAX'],
default='MAX',
help="set the stat pick method, MIN or MAX, [default is 'MAX']")
parser.add_argument(
'-x',
'--max',
dest='max',
metavar='INT',
type=int,
help=
"maximum of seqs for rarefaction, make sure that at least one sample's seq num "
"must over this number it can be overrited by STATFILE")
parser.add_argument('-t',
'--statfile',
dest='statfile',
metavar='FILE',
type=str,
default=None,
help="set the statfile produced by 01_stat.py")
parser.add_argument('-g',
'--group',
dest='group_file',
metavar='FILE',
type=str,
default=None,
help="set the group_file ")
args = parser.parse_args()
params = vars(args)
if params['statfile'] is not None:
maximum, minimum = parse_stat_file(params['statfile'],
group_file=params['group_file'])
print "maximum is :%s" % maximum
print "minimum is : %s" % minimum
if params['mode'] == 'MAX':
params['max'] = maximum
elif params['mode'] == 'MIN':
params['max'] = minimum
if params['max'] is None and params['statfile'] is None:
parser.print_help()
sys.exit()
return params