def params():
parser = ArgumentParser(description="Create file with coverage of a region")
parser = arguments.myargs(parser)
parser.add_argument("--region", help="bed file with regions.")
parser.add_argument("--reference", help="genome fasta file.")
parser.add_argument("--out", help="output file.")
parser.add_argument("bams", nargs="*", help="Bam files.")
parser.add_argument("--run", required=True, help="type of analysis", choices=['complete', 'report', 'metrics', 'basic-bam', 'cg-vcf', 'stats-coverage', 'tstv', 'bias-coverage', 'plot', 'fastqc', 'final'])
parser.add_argument("--n_sample", default=1000, help="sample bed files with this number of lines")
parser.add_argument("--seed", help="replication of sampling")
return parser
def test_cluster(self):
def fake_fn(n, args):
print 'inside function with %s' % n
time.sleep(n * 2)
start = time.time()
parser = ArgumentParser(description="Test cluster")
parser = arguments.myargs(parser)
args = parser.parse_args()
logger.info(args)
resources = {'name': 'step1', 'mem': 1, 'cores': 1}
cluster.send_job(fake_fn, [1, 2], args, resources)
logger.info('It took %.3f minutes without ipython' %
((time.time() - start) / 60))
samplenames = [os.path.splitext(os.path.basename(fn))[0] for fn in samples]
if isinstance(region_bed, six.string_types):
region_bed = pybedtools.BedTool(region_bed)
with file_transaction(out_file) as tx_out_file:
for line in region_bed:
chrom = line.chrom
start = max(line.start - PAD, 0)
end = line.end + PAD
df = _combine_regional_coverage(in_bams, samplenames, chrom,
start, end, os.path.dirname(tx_out_file))
df.to_csv(tx_out_file, mode='a', index=False, header=None)
return out_file
if __name__ == "__main__":
parser = ArgumentParser(description="Create file with coverage of a region")
parser = arguments.myargs(parser)
parser.add_argument("--region", help="bed file with regions.")
parser.add_argument("--reference", help="genome fasta file.")
parser.add_argument("--out", required=True, help="output file.")
parser.add_argument("bams", nargs="*", help="Bam files.")
parser.add_argument("--basic-bam", action="store_true", help="Calculate bam stats")
parser.add_argument("--basic-vcf", action="store_true", help="Calculate vcf stats")
parser.add_argument("--stats", action="store_true", help="Calculate stats for all regions.")
parser.add_argument("--tstv", action="store_true", help="Calculate ts/tv ratio.")
parser.add_argument("--bias", action="store_true", help="Calculate bias for all regions.")
parser.add_argument("--plot", action="store_true", help="Calculate nt coverage for given regions.")
parser.add_argument("--n_sample", default=1000, help="sample bed files with this number of lines")
parser.add_argument("--seed", help="replication of sampling")
args = parser.parse_args()
if os.path.exists(args.out):
import time
from argparse import ArgumentParser
from ichwrapper import arguments, cluster, fake
from ichwrapper.log import logger
if __name__ == "__main__":
start = time.time()
parser = ArgumentParser(description="Test cluster")
parser = arguments.myargs(parser)
parser.add_argument("--cmd", default=False, action='store_true')
args = parser.parse_args()
# args = parser.parse_args(["--parallel", "ipython", "--local"])
logger.info(args)
resources = {'name': 'step1', 'mem': 1, 'cores': 1}
data = [{'num': 1}, {'num': 2}]
data = cluster.update_samples(data, resources, args)
cluster.send_job(fake.fake_fn, data, args, resources)
if args.cmd:
cluster.send_job(fake.fake_cmd_fn, data, args, resources)
logger.info('It took %.3f minutes with ipython' % ((time.time()-start)/60))