Example #1
0
        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:
            
Example #4
0
        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