def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not opts.counts_fname:
parser.error("An otu table file must be specified")
if not opts.map_fname:
parser.error("A Map file must be specified")
prefs,data,background_color,label_color, ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
dir_path = opts.dir_path
if dir_path==None or dir_path=='':
dir_path = get_random_directory_name()
create_dir(dir_path)
create_dir(os.path.join(dir_path,"otu_network"))
create_dir(os.path.join(dir_path,"otu_network/props"))
create_dir(os.path.join(dir_path,"otu_network/stats"))
map_lines = open(opts.map_fname,'U').readlines()
otu_sample_lines = open(opts.counts_fname, 'U').readlines()
create_network_and_stats(dir_path,map_lines,otu_sample_lines,prefs,data,background_color,label_color)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs,data,background_color,label_color, ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
dir_path = opts.output_dir
create_dir(dir_path)
create_dir(os.path.join(dir_path,"otu_network"))
create_dir(os.path.join(dir_path,"otu_network/props"))
create_dir(os.path.join(dir_path,"otu_network/stats"))
map_lines = open(opts.map_fname,'U').readlines()
create_network_and_stats(dir_path,map_lines,opts.input_fp,prefs,data,background_color,label_color)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors = \
sample_color_prefs_and_map_data_from_options(opts)
dir_path = opts.output_dir
create_dir(dir_path)
create_dir(os.path.join(dir_path, "otu_network"))
create_dir(os.path.join(dir_path, "otu_network/props"))
create_dir(os.path.join(dir_path, "otu_network/stats"))
map_lines = open(opts.map_fname, 'U').readlines()
create_network_and_stats(dir_path, map_lines, opts.input_fp, prefs, data,
background_color, label_color)
