def normalize_CSS(input_path, out_path, output_CSS_statistics):
 tmp_bt = load_table(input_path)
 if output_CSS_statistics:
  (base_fname, ext) = splitext(out_path)
  output_CSS_statistics = (base_fname + '_CSS_statistics.txt')
 with tempfile.NamedTemporaryFile(dir=get_qiime_temp_dir(), prefix='QIIME-normalize-table-temp-table-', suffix='.biom') as temp_fh:
  temp_fh.write(tmp_bt.to_json('forR'))
  temp_fh.flush()
  run_CSS(temp_fh.name, out_path, output_CSS_statistics=output_CSS_statistics)

def normalize_CSS ( input_path , out_path , output_CSS_statistics ) : tmp_bt = load_table ( input_path ) if output_CSS_statistics : ( base_fname , ext ) = splitext ( out_path ) output_CSS_statistics = ( base_fname + '_CSS_statistics.txt' ) with tempfile . NamedTemporaryFile ( dir = get_qiime_temp_dir ( ) , prefix = 'QIIME-normalize-table-temp-table-' , suffix = '.biom' ) as temp_fh : temp_fh . write ( tmp_bt . to_json ( 'forR' ) ) temp_fh . flush ( ) run_CSS ( temp_fh . name , out_path , output_CSS_statistics = output_CSS_statistics )
performs metagenomeseqs css normalization on a single raw abundance otu matrix .