def preprocess_on_cluster(sff_fps, log_fp, fasta_fp=None, out_fp='/tmp/', squeeze=False, verbose=False, primer=STANDARD_BACTERIAL_PRIMER):
 cmd = ('denoiser_preprocess.py -i %s -l %s -o %s' % (','.join(sff_fps), log_fp, out_fp))
 if fasta_fp:
  cmd += (' -f %s' % fasta_fp)
 if squeeze:
  cmd += ' -s'
 if verbose:
  cmd += ' -v'
 if primer:
  cmd += (' -p %s' % primer)
 submit_jobs([cmd], ('pp_' + make_tmp_name(6)))
 wait_for_file((out_fp + '/prefix_mapping.txt'), 10)

def preprocess_on_cluster ( sff_fps , log_fp , fasta_fp = None , out_fp = '/tmp/' , squeeze = False , verbose = False , primer = STANDARD_BACTERIAL_PRIMER ) : cmd = ( 'denoiser_preprocess.py -i %s -l %s -o %s' % ( ',' . join ( sff_fps ) , log_fp , out_fp ) ) if fasta_fp : cmd += ( ' -f %s' % fasta_fp ) if squeeze : cmd += ' -s' if verbose : cmd += ' -v' if primer : cmd += ( ' -p %s' % primer ) submit_jobs ( [ cmd ] , ( 'pp_' + make_tmp_name ( 6 ) ) ) wait_for_file ( ( out_fp + '/prefix_mapping.txt' ) , 10 )
call preprocess via cluster_jobs_script on the cluster .