def common_updates(self, args):
if args.config is not None:
config = Config.load(args.config)
else:
try:
config = Config.load('./sgains.yml')
except AssertionError:
config = Config.default()
self.config = config
if args.dry_run is not None:
self.config.dry_run = args.dry_run
if args.force is not None:
self.config.force = args.force
if args.parallel is not None:
self.config.parallel = args.parallel
def test_bins_config():
conf = Config.load("tests/data/scpipe_tests.yml")
assert conf is not None
assert conf.mappable_regions is not None
assert conf.mappable_regions.length == 100
assert conf.bins is not None
assert conf.bins.bins_count == 10000
assert conf.bins.bins_dir == "test_data/R100_B10k"
def test_pickle_depickle():
conf = Config.load("tests/data/scpipe_tests.yml")
assert conf is not None
pkl = pickle.dumps(conf)
assert pkl is not None
res = pickle.loads(pkl)
assert res is not None
assert isinstance(res, Config)
assert conf.to_dict() == res.to_dict()
def hg():
config = Config.load("tests/data/scpipe_tests.yml", use_config_dir=True)
return Genome(config)
def tests_config():
config = Config.load("tests/data/scpipe_tests.yml", use_config_dir=True)
return config
subprocess.check_call(
[
'Rscript',
rscript,
scclust_dirname,
case_name,
varbin_dir,
varbin_suffix,
bin_boundaries_filename,
cytoband,
str(nsim),
str(sharemin),
str(fdrthres),
str(nshare),
str(climbtoshare),
],
shell=False,
stdout=sys.stdout,
stderr=sys.stdout,
# stdout=shutup, stderr=shutup,
)
if __name__ == "__main__":
config = Config.load("sgains.yml")
print(config)
pipeline = Rpipeline(config)
pipeline.run()
def main(argv=None):
if argv is None:
argv = sys.argv
else:
argv.extend(sys.argv)
# Setup argument parser
program_name = os.path.basename(sys.argv[0])
program_shortdesc = \
'sgains - sparse genomic analysis of individual nuclei by ' \
'sequencing pipeline'
program_description = '''%s
USAGE
''' % (program_shortdesc, )
try:
import setproctitle # @UnresolvedImport
setproctitle.setproctitle('sgains')
except ImportError:
pass
try:
defaults_config = Config.parse_args(argv)
argparser = ArgumentParser(
description=program_description,
formatter_class=RawDescriptionHelpFormatter)
OptionsBase.common_options(argparser)
subparsers = argparser.add_subparsers(
title="subcommands"
)
process_command = ProcessCommand(
argparser, subparsers)
process_command.add_options(defaults_config)
prepare_command = PrepareCommand(
argparser, subparsers)
prepare_command.add_options(defaults_config)
genomeindex_command = GenomeIndexCommand(
argparser, subparsers)
genomeindex_command.add_options(defaults_config)
mappable_regions_command = MappableRegionsCommand(
argparser, subparsers)
mappable_regions_command.add_options(defaults_config)
bins_command = BinsCommand(
argparser, subparsers)
bins_command.add_options(defaults_config)
mapping_command = MappingCommand(
argparser, subparsers)
mapping_command.add_options(defaults_config)
varbin_command = VarbinCommand(
argparser, subparsers)
varbin_command.add_options(defaults_config)
scclust_command = SCclustCommand(
argparser, subparsers)
scclust_command.add_options(defaults_config)
args = argparser.parse_args(argv[1:])
args.func(args)
return 0
except KeyboardInterrupt:
traceback.print_exc()
return 0
except Exception as e:
traceback.print_exc()
indent = len(program_name) * " "
sys.stderr.write(program_name + ": " + repr(e) + "\n")
sys.stderr.write(indent + " for help use --help")
sys.stderr.write('\n')
return 2
def test_load_config():
conf = Config.load("tests/data/scpipe_tests.yml")
assert conf is not None
assert conf.genome is not None
assert os.path.basename(conf.genome.version) == "hg19"
def tests_config():
config = Config.load("tests/data/scpipe_tests.yml")
return config