def normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero):
 tmp_bt = load_table(input_path)
 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_DESeq2(temp_fh.name, out_path, DESeq_negatives_to_zero)

def normalize_DESeq2 ( input_path , out_path , DESeq_negatives_to_zero ) : tmp_bt = load_table ( input_path ) 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_DESeq2 ( temp_fh . name , out_path , DESeq_negatives_to_zero )
performs deseq2vs normalization on a single raw abundance otu matrix .