def go(self, skip_dry_run=False):
"""Do the actual running"""
if self.save_workflow_graph or (not skip_dry_run):
self.dry_run()
if self.dry_run_only:
return
# snakemake.main() accepts an `argv` parameter, but then the code has mixed responses to
# that, and at places continues to read from sys.argv in a hardcoded manner. so we have to
# overwrite our argv here.
original_sys_argv = copy.deepcopy(sys.argv)
sys.argv = ['snakemake',
'--snakefile',
get_workflow_snake_file_path(self.args.workflow),
'--configfile',
self.args.config_file]
if self.additional_params:
sys.argv.extend(self.additional_params)
if self.list_dependencies:
sys.argv.extend(['--dryrun', '--printshellcmds'])
snakemake.main()
sys.exit(0)
else:
sys.argv.extend(['-p'])
snakemake.main()
# restore the `sys.argv` to the original for the sake of sakity (totally made up word,
# but you already know what it measn. you're welcome.)
sys.argv = original_sys_argv
def go(self, skip_dry_run=False):
"""Do the actual running"""
if self.save_workflow_graph or (not skip_dry_run):
self.dry_run()
if self.dry_run_only:
return
# snakemake.main() accepts an `argv` parameter, but then the code has mixed responses to
# that, and at places continues to read from sys.argv in a hardcoded manner. so we have to
# overwrite our argv here.
original_sys_argv = copy.deepcopy(sys.argv)
sys.argv = [
'snakemake', '--snakefile',
get_workflow_snake_file_path(self.args.workflow), '--configfile',
self.args.config_file
]
if self.additional_params:
sys.argv.extend(self.additional_params)
if self.list_dependencies:
sys.argv.extend(['--dryrun', '--printshellcmds'])
snakemake.main()
sys.exit(0)
else:
sys.argv.extend(['-p'])
snakemake.main()
# restore the `sys.argv` to the original for the sake of sakity (totally made up word,
# but you already know what it measn. you're welcome.)
sys.argv = original_sys_argv
def run(self):
'''
Run the wrapped command or workflow.
'''
# Overwrite the generic method, because we have to use the snakemake API
try:
snakemake.main(self.remaining[1:])
except SystemExit:
# snakemake main wants to exit ... but we want to write the xml files first
return
def main(**config):
"""
Main function of pancovcorrect
Parameter:
config: A dict pass to snakemake as config.
Value associate to 'snakemake' is parse with snakemake cli parser.
Return:
True if workflow execution was successful.
"""
params = config["snakemake"]
del config["snakemake"]
# Found Snakefile
params.extend(
[
"--snakefile",
os.path.join(os.path.dirname(__file__), f"{package_name}.snk"),
]
)
# Add parameter with config
params.append("--config")
for (name, value) in config.items():
params.append(f"{name}={value}")
# Add target
params.extend(["--", "all"])
return snakemake.main(params)
def proxy_to_snakemake(tailseeker_dir):
from snakemake import main
tailseeker_main_file = os.path.join(tailseeker_dir, 'tailseeker', 'main.py')
if '-s' not in sys.argv and '--snakefile' not in sys.argv:
sys.argv.insert(1, '-s')
sys.argv.insert(2, tailseeker_main_file)
sys.exit(main())
def proxy_to_snakemake(tailseeker_dir):
from snakemake import main
tailseeker_main_file = os.path.join(tailseeker_dir, 'tailseeker',
'main.py')
if '-s' not in sys.argv and '--snakefile' not in sys.argv:
sys.argv.insert(1, '-s')
sys.argv.insert(2, tailseeker_main_file)
sys.exit(main())
# This script makes it possible to invoke snakemake with 'python3 -m snakemake' from snakemake import main main()
def __call__(self, parser, namespace, values, option_string=None):
snakemake.main(["-h"])
def proxy_to_snakemake(tailseeker_dir):
from snakemake import main
tailseeker_main_file = os.path.join(tailseeker_dir, 'tailseeker', 'main.py')
if '-s' not in sys.argv and '--snakefile' not in sys.argv:
sys.argv.insert(1, '-s')
sys.argv.insert(2, tailseeker_main_file)
sys.exit(main())
def show_banner():
if os.environ.get('TAILSEEKER_SKIP_BANNER', 'no') == 'no':
print("""\
Tailseeker {version} - High-throughput measurement of poly(A) tails
""".format(version=tailseeker.__version__))
def main(tailseeker_dir):
show_banner()
os.environ['TAILSEEKER_DIR'] = tailseeker_dir
os.environ['TAILSEEKER_SKIP_BANNER'] = 'yes'
check_configuration()
proxy_to_snakemake(tailseeker_dir)
if __name__ == '__main__':
main()
def main_full():
snakefile = get_snakefile()
options = argv[1:]
options.append("-s")
options.append(snakefile)
snakemake.main(options)
#!/Library/Frameworks/Python.framework/Versions/3.5/bin/python3
# -*- coding: utf-8 -*-
import re
import sys
from snakemake import main
if __name__ == '__main__':
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
sys.exit(main())
