def __init__(self, profile, taxfile, outfile, group_file=None, expand=1):
self.table = TableParser(profile)
self.otu_tax = TaxParser(taxfile)
self.group = parse_group_file(group_file)
if self.group is not None:
self.groups = list(set(self.group.itervalues()))
else:
self.groups = None
self.outfile = outfile
self.expand = expand
self.tax_level = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
self.tax_dict = {
'k': 'kingdom',
'p': 'phylum',
'c': 'class',
'o': 'order',
'f': 'family',
'g': 'genus',
's': 'species',
}
self.samples = {}
self.node_list = {}
self.root_nodes = {}
parser = argparse.ArgumentParser(
description='get otu profile uniform | v1.0 at 2015/09/29 by liangzb')
parser.add_argument(
'-i',
'--infile',
dest='infile',
metavar='FILE',
type=str,
required=True,
help="set the un-uniformed profile produced by biom convert")
parser.add_argument('-o',
'--out_file',
dest='outfile',
metavar='FILE',
type=str,
required=True,
help="set the output uniform profile")
args = parser.parse_args()
params = vars(args)
return params
if __name__ == '__main__':
params = read_params(sys.argv)
mkdir(os.path.dirname(params['outfile']))
table = TableParser(params['infile'])
table.parse_table()
table.get_uniform()
table.write_table(params['outfile'])
