def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
output_dir = opts.output_dir
create_dir(output_dir)
otu_table_fp = opts.otu_table
otu_table = load_table(otu_table_fp)
tree_fh = open(opts.tree_file, 'U')
tree = DndParser(tree_fh)
tree_fh.close()
mapping_fp = opts.mapping_fp
if mapping_fp:
mapping_f = open(mapping_fp, 'U')
input_map_basename = splitext(split(mapping_fp)[1])[0]
else:
mapping_f = None
input_map_basename = None
input_table_basename = splitext(split(otu_table_fp)[1])[0]
simsam_range_to_files(otu_table,
tree,
simulated_sample_sizes=map(int, opts.num.split(',')),
dissimilarities=map(float, opts.dissim.split(',')),
output_dir=output_dir,
mapping_f=mapping_f,
output_table_basename=input_table_basename,
output_map_basename=input_map_basename)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
output_dir = opts.output_dir
create_dir(output_dir)
otu_table_fp = opts.otu_table
otu_table_fh = open(otu_table_fp, 'U')
otu_table = parse_biom_table(otu_table_fh)
otu_table_fh.close()
tree_fh = open(opts.tree_file, 'U')
tree = DndParser(tree_fh)
tree_fh.close()
mapping_fp = opts.mapping_fp
if mapping_fp:
mapping_f = open(mapping_fp, 'U')
input_map_basename = splitext(split(mapping_fp)[1])[0]
else:
mapping_f = None
input_map_basename = None
input_table_basename = splitext(split(otu_table_fp)[1])[0]
simsam_range_to_files(otu_table,
tree,
simulated_sample_sizes=map(int, opts.num.split(',')),
dissimilarities=map(float, opts.dissim.split(',')),
output_dir=output_dir,
mapping_f=mapping_f,
output_table_basename=input_table_basename,
output_map_basename=input_map_basename)