for fragment in fragments_sample: # Submit to the cluster self if requested if submit: fork_self(seq_run, adaID, fragment, block_len_initial, n_reads_per_ali, store_allele_counts, VERBOSE=VERBOSE) continue if summary: sfn = get_build_consensus_summary_filename(data_folder, adaID, fragment, iterative=False) with open(sfn, 'w') as f: f.write('Call: python build_consensus.py'+\ ' --run '+seq_run+\ ' --adaIDs '+adaID+\ ' --fragments '+fragment+\ ' --block-length '+str(block_len_initial)+\ ' --reads-per-alignment '+str(n_reads_per_ali)+\ ' --verbose '+str(VERBOSE)) if store_allele_counts: f.write(' --allele-counts') f.write('\n') if VERBOSE: print seq_run, adaID, fragment
if 'genomewide' in fragments: fragments_sample.append('genomewide') if VERBOSE >= 3: print 'adaID '+adaID+': fragments '+' '.join(fragments_sample) for fragment in fragments_sample: # Submit to the cluster self if requested if submit: fork_self(seq_run, adaID, fragment, block_len_initial, n_reads_per_ali, store_allele_counts, VERBOSE=VERBOSE) continue if summary: sfn = get_build_consensus_summary_filename(data_folder, adaID, fragment, iterative=False) with open(sfn, 'w') as f: f.write('Call: python build_consensus.py'+\ ' --run '+seq_run+\ ' --adaIDs '+adaID+\ ' --fragments '+fragment+\ ' --block-length '+str(block_len_initial)+\ ' --reads-per-alignment '+str(n_reads_per_ali)+\ ' --verbose '+str(VERBOSE)) if store_allele_counts: f.write(' --allele-counts') f.write('\n') if VERBOSE: print seq_run, adaID, fragment if fragment == 'genomewide':
if VERBOSE >= 3: print 'adaID '+adaID+': fragments '+' '.join(fragments_sample) make_output_folders(data_folder, adaID, VERBOSE=VERBOSE) for fragment in fragments_sample: # Submit to the cluster self if requested if submit: fork_self(seq_run, adaID, fragment, n_reads, iterations_max, VERBOSE=VERBOSE) continue if summary: sfn = get_build_consensus_summary_filename(data_folder, adaID, fragment) with open(sfn, 'w') as f: f.write('Call: python build_consensus_iterative.py'+\ ' --run '+seq_run+\ ' --adaIDs '+adaID+\ ' --fragments '+fragment+\ ' --iterations '+str(iterations_max)+\ ' -n '+str(n_reads)+\ ' --verbose '+str(VERBOSE)) f.write('\n') # Iterate the consensus building until convergence n_iter = 1 while True:
make_output_folders(data_folder, adaID, VERBOSE=VERBOSE) for fragment in fragments_sample: # Submit to the cluster self if requested if submit: fork_self(seq_run, adaID, fragment, n_reads, iterations_max, VERBOSE=VERBOSE) continue if summary: sfn = get_build_consensus_summary_filename( data_folder, adaID, fragment) with open(sfn, 'w') as f: f.write('Call: python build_consensus_iterative.py'+\ ' --run '+seq_run+\ ' --adaIDs '+adaID+\ ' --fragments '+fragment+\ ' --iterations '+str(iterations_max)+\ ' -n '+str(n_reads)+\ ' --verbose '+str(VERBOSE)) f.write('\n') # Iterate the consensus building until convergence n_iter = 1 while True: # The first iteration comes from a mapping already