) cmd += 'cd {mount}/input; '.format(mount=mount) cmd += 'bwa mem -t {cores} {reference} {fastq} > {mount}/{output}; '.format( cores=cores, reference=os.path.basename(reference), fastq=' '.join([mount + '/input/' + os.path.basename(f) for f in fastq]), mount=mount, output='output/aligned.sam' ) # Add any extra flags if they are passed if extra_command_flags: cmd += ' {}'.format(extra_command_flags) p.command = cmd # Build the BWA pipeline configuration p.build() # =================================================== # Execute the pipeline # --------------------------------------------------- operation = p.run() # Printout the response to SDTOUT sys.stdout.write('Pipeline Response:\n') sys.stdout.write(json.dumps(operation, indent=4, sort_keys=True)) sys.stdout.write('\n') if __name__ == "__main__": main()
logging.warning('Sample {} has no coverage for target {}.'.format(subject['sample'], targetCol)) if errors > 0: sys.exit(1) # Compute the logistic normal hyperparameters. # Omit the non-target columns. mu, covariance = hln_EM(coverage_df[targetCols].values.astype(float), max_iterations=max_iterations, tol=tol, fit_diag_only=fit_diag_only) # Pickle the intervals, hyperparameters and CoverageMatrix arguments into the outputFile. logging.info('Trained for {} total targets'.format(len(targets))) logging.info('Writing intervals plus hyperparameters to file {}.'.format(outputFile)) targets_params['parameters'] = HLN_Parameters(targets, mu, covariance) with open(outputFile, 'w') as f: cPickle.dump(targets_params, f, protocol=cPickle.HIGHEST_PROTOCOL) @command('create-bams') def create_bams(targetsFile, outputPrefix): """Makes simulated data to run the program with, given a target bed file and an output file prefix. :param targetsFile: A BED file with targets to simulate coverage for. :param outputPrefix: an output file prefix used to name the output bam and fofn file. :return: """ SimulateData.make_simulated_data(outputPrefix, targetsFile) if __name__ == '__main__': main()
def main(): """Set debug and run mando.main function.""" if not os.path.exists("debug_tstoolbox"): sys.tracebacklimit = 0 mando.main()
def main(): if not os.path.exists('debug_swmmtoolbox'): sys.tracebacklimit = 0 mando.main()
def main(): mando.main()
def main(): ''' Main function ''' if not os.path.exists('debug_wdmtoolbox'): sys.tracebacklimit = 0 mando.main()
def main(): """Main function.""" if not os.path.exists('debug_wdmtoolbox'): sys.tracebacklimit = 0 mando.main()
def main(): if not os.path.exists("debug_hspfbintoolbox"): sys.tracebacklimit = 0 mando.main()
def main(): ''' Main ''' if not os.path.exists('debug_mettoolbox'): sys.tracebacklimit = 0 mando.main()
def main(): """Run the main function.""" if not os.path.exists('debug_wdmtoolbox'): sys.tracebacklimit = 0 mando.main()
def main(): """Set debug and run mando.main function.""" if not os.path.exists('debug_tstoolbox'): sys.tracebacklimit = 0 mando.main()
def main(): """Run the main function.""" if not os.path.exists("debug_wdmtoolbox"): sys.tracebacklimit = 0 mando.main()