)
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():
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()
