'--annot_stem', args.annot_stem, 'main', '--chrnum', '$LSB_JOBINDEX'
]
outfilepath = \
args.annot_stem + '.random.%I.creation.log'
bsub.submit(
['python', '-u', paths.code + 'munge/randomize_annot_signs.py'] +
my_args,
outfilepath,
jobname='randomize[1-22]',
debug=args.debug)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--annot_stem', type=str, required=True,
help='path to annot file, not including chromosome number and extension. ' + \
'For example: path/to/annot')
main_parser, submit_parser = bsub.add_main_and_submit(parser, main, submit)
main_parser.add_argument('--chrnum',
type=int,
required=True,
help='chromosome to analyze')
submit_parser.add_argument('-debug',
action='store_true',
default=False,
help='do not actually submit the jobs')
bsub.choose_parser_and_run(parser)
# est.run_realdata('')
def submit(args):
my_args = ['main', '--chrom', '$LSB_JOBINDEX']
d = Dataset('UK10Khg19.22')
outfilepath = d.auxfiles_path + '../' + \
'%I/.preprocess.out'
bsub.submit(['python', '-u', paths.code + 'real/preprocess.py'] + my_args,
outfilepath,
jobname='preprocess[1-22]',
memory_GB=16)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
subparser_main, subparser_submit = bsub.add_main_and_submit(
parser, main, submit)
subparser_main.add_argument('--chrom',
type=int,
required=True,
help='the chromosome to preprocess')
subparser_main.add_argument(
'--chunk',
type=int,
required=True,
help='the chunk of the chromosome to process (1-indexed)')
bsub.choose_parser_and_run(parser)
print('submitting', s.name)
my_args = ['--exp-name', args.exp_name] + \
['main',
'--sim-name', s.name,
'--beta-num', '$LSB_JOBINDEX']
outfilename = s.root_folder(create=True) + '.sim_sumstats.%I'
bsub.submit(['python', '-u', __file__] + my_args,
outfilename,
# queue='medium', time_in_hours=40,
queue='short', time_in_hours=12,
jobname=s.name+'.simsumstats[1-{}]'.format(s.num_betas),
debug=args.debug)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--exp-name', type=str, required=True,
help='name of the experiment file containing simulations, without ext')
main_parser, submit_parser = bsub.add_main_and_submit(parser, main, submit)
main_parser.add_argument('--sim-name', type=str, required=True,
help='name of the simulation to run inside the experiment json file')
main_parser.add_argument('--beta-num', type=int, required=True,
help='index of the beta to simulate. 1-indexed!')
submit_parser.add_argument('-debug', action='store_true', default=False)
bsub.choose_parser_and_run(parser)
num_chunks=500,
chunk=args.chunk)
print(est.chunks_containing_region())
# est.run_realdata('')
def submit(args):
my_args = ['main',
'--chrom', '$LSB_JOBINDEX']
d = Dataset('UK10Khg19.22')
outfilepath = d.auxfiles_path + '../' + \
'%I/.preprocess.out'
bsub.submit(
['python', '-u', paths.code + 'real/preprocess.py'] + my_args,
outfilepath,
jobname='preprocess[1-22]',
memory_GB=16)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
subparser_main, subparser_submit = bsub.add_main_and_submit(parser,
main,
submit)
subparser_main.add_argument('--chrom', type=int, required=True,
help='the chromosome to preprocess')
subparser_main.add_argument('--chunk', type=int, required=True,
help='the chunk of the chromosome to process (1-indexed)')
bsub.choose_parser_and_run(parser)