def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
mapping_fp = opts.mapping_fp
collapse_fields = opts.collapse_fields.split(',')
input_biom_fp = opts.input_biom_fp
collapse_mode = opts.collapse_mode
output_biom_fp = opts.output_biom_fp
output_mapping_fp = opts.output_mapping_fp
normalize = opts.normalize
collapsed_metadata, collapsed_table = \
collapse_samples(load_table(input_biom_fp),
open(mapping_fp, 'U'),
collapse_fields,
collapse_mode)
if normalize:
collapsed_table.norm(axis='sample', inplace=True)
write_biom_table(collapsed_table, output_biom_fp)
output_map_lines = mapping_lines_from_collapsed_df(collapsed_metadata)
with open(output_mapping_fp, 'w') as output_mapping_f:
output_mapping_f.write('\n'.join(output_map_lines))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
mapping_fp = opts.mapping_fp
collapse_fields = opts.collapse_fields.split(',')
input_biom_fp = opts.input_biom_fp
collapse_mode = opts.collapse_mode
output_biom_fp = opts.output_biom_fp
output_mapping_fp = opts.output_mapping_fp
normalize = opts.normalize
collapsed_metadata, collapsed_table = \
collapse_samples(load_table(input_biom_fp),
open(mapping_fp, 'U'),
collapse_fields,
collapse_mode)
if normalize:
collapsed_table.norm(axis='sample', inplace=True)
write_biom_table(collapsed_table, output_biom_fp)
output_map_lines = mapping_lines_from_collapsed_df(collapsed_metadata)
with open(output_mapping_fp, 'w') as output_mapping_f:
output_mapping_f.write('\n'.join(output_map_lines))