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#!/usr/bin/env python
# File created on 19 Mar 2011
from __future__ import division
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from qiime.util import make_option
from cogent.parse.tree import DndParser
from qiime.parse import parse_otu_table
from qiime.util import parse_command_line_parameters
from qiime.format import format_otu_table
from qiime.simsam import sim_otu_table
script_info = {}
script_info['brief_description'] = "Simulate samples for each sample in an OTU table, using a phylogenetic tree."
script_info['script_description'] = ""
script_info['script_usage'] = [("","Make 3 related sample for each sample in in_otu_table.txt.","%prog -i in_otu_table.txt -t rep_set.tre -o out_otu_table.txt -d .001 -n 3")]
script_info['output_description']= "an otu table, samples are named: 'original_sample_0, original_sample_1 ...'"
script_info['required_options'] = [
make_option('-i','--otu_table',help='the input otu table'),
make_option('-t','--tree_file',help='tree file'),
make_option('-o','--output_file',help='the output file'),
make_option('-d','--dissim',help='dissimilarity between nodes up the tree',
type=float),
make_option('-n','--num',
help='number of simulated samples per input sample',
type=int)
]
script_info['optional_options'] = []
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
out_fh = open(opts.output_file,'w')
otu_table_fh = open(opts.otu_table,'U')
sample_ids, otu_ids, otu_mtx, otu_metadata = parse_otu_table(otu_table_fh)
tree_fh = open(opts.tree_file,'U')
tree = DndParser(tree_fh)
res_sam_names, res_otus, res_otu_mtx, res_otu_metadata = \
sim_otu_table(sample_ids, otu_ids, otu_mtx, otu_metadata,
tree, opts.num, opts.dissim)
out_fh.write(format_otu_table(res_sam_names, res_otus,
res_otu_mtx, res_otu_metadata))
if __name__ == "__main__":
main()
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