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))
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')
otu_table = parse_biom_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(otu_table.SampleIds, otu_table.ObservationIds, otu_table.iterSamples(),
otu_table.ObservationMetadata, tree, opts.num, opts.dissim)
rich_table = table_factory(res_otu_mtx,res_sam_names,res_otus,
observation_metadata=res_otu_metadata)
out_fh.write(format_biom_table(rich_table))
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')
otu_table = parse_biom_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(otu_table.SampleIds, otu_table.ObservationIds, otu_table.iterSamples(),
otu_table.ObservationMetadata, tree, opts.num, opts.dissim)
rich_table = table_factory(res_otu_mtx,
res_sam_names,
res_otus,
observation_metadata=res_otu_metadata)
out_fh.write(format_biom_table(rich_table))