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))