def read_params(args):
parser = argparse.ArgumentParser(description='a wrapper for LEfSe | v1.0 at 2017/1/23 by huangy')
parser.add_argument('-i', '--summarize_all', dest='infile', metavar='FILE', type=str, required=True,
help="set hte otu_table_all.txt produced by 02_summarize_trans.py")
parser.add_argument('-l', '--LEfSe_path', dest='LEfSe_path', metavar='DIR', type=str, default=None,
help="set the LEfSe path, default find in env")
parser.add_argument('-g', '--group_file', dest='group', metavar='FILE', type=str, required=True,
help="set the group file")
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='DIR', type=str, required=True,
help="set the output dir")
parser.add_argument('--LDA', dest='LDA', metavar='FLOAT', type=float, default=2,
help="set the LDA cutoff, [default is 2]")
parser.add_argument('--class_row', dest='c', metavar='INT', type=int, default=1,
help="set the class row, [default is 1]")
parser.add_argument('--subject_row', dest='u', metavar='INT', type=int, default=2,
help="set the subject row, [default is 2]")
parser.add_argument('--quantile',dest="quantile",metavar='FLOAT',type=float,default=0)
parser.add_argument('--cut_off',dest='cut_off',metavar='FLOAT',type=float,default=1e-20)
args = parser.parse_args()
params = vars(args)
params['groupDir'] = params['group']
params['group'] = parse_group_file(params['group'])
if params['LEfSe_path'] is None:
params['LEfSe_path'] = ''
else:
params['LEfSe_path'] += '/'
return params
def read_params(args):
parser = argparse.ArgumentParser(description='a wrapper for LEfSe | v1.0 at 2015/10/19 by liangzb')
parser.add_argument('-i', '--summarize_all', dest='infile', metavar='FILE', type=str, required=True,
help="set hte otu_table_all.txt produced by 02_summarize_trans.py")
parser.add_argument('-l', '--LEfSe_path', dest='LEfSe_path', metavar='DIR', type=str, default=None,
help="set the LEfSe path, default find in env")
parser.add_argument('-g', '--group_file', dest='group', metavar='FILE', type=str, required=True,
help="set the group file")
parser.add_argument('-o', '--out_dir', dest='out_dir', metavar='DIR', type=str, required=True,
help="set the output dir")
parser.add_argument('--LDA', dest='LDA', metavar='FLOAT', type=float, default=2,
help="set the LDA cutoff, [default is 2]")
parser.add_argument('--class_row', dest='c', metavar='INT', type=int, default=1,
help="set the class row, [default is 1]")
parser.add_argument('--subject_row', dest='u', metavar='INT', type=int, default=2,
help="set the subject row, [default is 2]")
parser.add_argument('--quantile',dest="quantile",metavar='FLOAT',type=float,default=0)
parser.add_argument('--cut_off',dest='cut_off',metavar='FLOAT',type=float,default=1e-20)
args = parser.parse_args()
params = vars(args)
params['groupDir'] = params['group']
params['group'] = parse_group_file(params['group'])
if params['LEfSe_path'] is None:
params['LEfSe_path'] = ''
else:
params['LEfSe_path'] += '/'
return params
def read_params(args):
parser = argparse.ArgumentParser(description='''otu venn analysis | v1.0 at 2015/10/13 by liangzb ''')
parser.add_argument('-i', '--microbial_profile', dest='microbial_profile', metavar='FILE', type=str, required=True,
help="set the otu table file")
parser.add_argument('-g', '--group_file', dest='group', metavar='FILE', type=str, required=True,
help="set the group file")
parser.add_argument('-o', '--outputdir', dest='outputdir', metavar='DIR', type=str, required=True,
help="set the output DIR")
args = parser.parse_args()
params = vars(args)
params['group_dir'] = params['group']
params['group'] = parse_group_file(params['group'])
return params
def read_params(args):
parser = argparse.ArgumentParser(description='tax bar plot | v1.0 at 2015/11/06 by liangzb')
parser.add_argument('-i', '--inputfile', dest='inputfile', metavar='FILE', type=str, required=True,
help="input micbiom abundance file")
parser.add_argument('-g', '--group', dest='group', metavar='FILE', type=str, default=None,
help="set the group_file")
parser.add_argument('-o', '--outputfile', dest='outputfile', metavar='FILE', type=str, required=True,
help="set the output file")
parser.add_argument('-t','--title',dest='title',metavar='STRING',type=str,required=True,
help="set title of plot")
parser.add_argument('--with_group', dest='with_group', action='store_true',
help="plot group bar plot, if group is not set, this param will not be used")
parser.add_argument('--without_group', dest="with_group", action='store_false',
help="plot sample bar plot, if this params is set, group file will only for order")
parser.add_argument('--contains_other', dest="contains_other", action='store_true',
help="totel abundance contains other abundance ; totel aundance is 1")
parser.add_argument('--top', dest="top",metavar="INT",type=int,default=20,
help='set the top num, [default is 20]')
parser.set_defaults(with_group=False)
args = parser.parse_args()
params = vars(args)
params['group'] = parse_group_file(params['group'])
return params
with open (file) as fqin:
first_line = fqin.readline()
for lines in fqin:
tab = lines.strip().split()
if tab[0] in group:
group_name = group[tab[0]]
tab[1] = tab[1].replace(',','')
if group_name not in alphas:
alphas[group_name] = []
alphas[group_name].append(tab[1])
else:
alphas[group_name].append(tab[1])
return alphas
def write_f(alphas,out_file):
with open(out_file,"w") as out:
for group_name in alphas:
num_gene = "\t".join(alphas[group_name])
out.write('%s\t%s\n' % (group_name, num_gene))
if __name__ == "__main__":
reload(sys)
sys.setdefaultencoding('utf8')
params = read_params(sys.argv)
in_file = params["all_gene_alpha_div"]
out_file = params["out_file"]
group = parse_group_file(params["group"])
alphas = opt_group(in_file, group)
write_f(alphas, out_file)
