def check_access(json, username, password, url, filename, cwd, config):
if json:
json = os.path.join(cwd, json)
gfunk.add_arg_to_config("json", json, config)
gfunk.add_arg_to_config("username", username, config)
gfunk.add_arg_to_config("password", password, config)
gfunk.add_arg_to_config("url", url, config)
gfunk.add_arg_to_config("filename", filename, config)
if not config["json"] and config["analysis"] == "full":
if not config["username"] or not config["password"] or not config[
"url"] or not config["filename"]:
sys.stderr.write(
cyan(
f'Error: please either provide a json file, a metadata file (with analysis option `report_only`) or the correct gisaid access information.\n'
))
sys.exit(-1)
if not config["metadata"] and config["analysis"] == "report_only":
sys.stderr.write(
cyan(
f'Error: please provide a metadata file (with analysis option `report_only`) or the correct gisaid access information, or a json file of gisaid data.\n'
))
sys.exit(-1)
elif config["metadata"]:
config["metadata"] = os.path.join(cwd, config["metadata"])
if not os.path.exists(config["metadata"]):
sys.stderr.write(
cyan(f'Error: metadata input file not found ') +
f"{config['metadata']}\n")
sys.exit(-1)
def check_dependencies():
missing = []
dependency_list = ["gofasta", "minimap2", "snakemake", "usher", "pangolin"]
module_list = [
"Bio", "sklearn", "pandas", "joblib", "pysam", "pangoLEARN",
"reportfunk", "datafunk", "fastafunk", "constellations"
]
for dependency in dependency_list:
check_this_dependency(dependency, missing)
for module in module_list:
check_module(module, missing)
if missing:
if len(missing) == 1:
sys.stderr.write(
cyan(f'Error: Missing dependency `{missing[0]}`.') +
'\nPlease update your grinch environment.\n')
sys.exit(-1)
else:
dependencies = ""
for i in missing:
dependencies += f"\t- {i}\n"
sys.stderr.write(
cyan(f'Error: Missing dependencies.') +
f'\n{dependencies}Please update your grinch environment.\n')
sys.exit(-1)
else:
print(green("All dependencies satisfied."))
def get_report_snakefile(thisdir):
snakefile = os.path.join(thisdir, 'scripts', 'render_report.smk')
if not os.path.exists(snakefile):
sys.stderr.write(
cyan(
f'Error: cannot find Snakefile at {snakefile}\n Check installation\n'
))
sys.exit(-1)
return snakefile
def package_data_check(filename, directory, key, config):
try:
package_datafile = os.path.join(directory, filename)
data = pkg_resources.resource_filename('grinch', package_datafile)
config[key] = data
except:
sys.stderr.write(
cyan(f'Error: Missing package data.') +
f'\n\t- {filename}\nPlease install the latest grinch version with `grinch --update`.\n'
)
sys.exit(-1)
def main(sysargs=sys.argv[1:]):
parser = argparse.ArgumentParser(
prog=_program, usage='''grinch -i <config.yaml> [options]''')
io_group = parser.add_argument_group('input output options')
io_group.add_argument(
'-a',
"--analysis",
action="store",
help="Analysis entry point: `full` or `report_only`. Default: `full`",
dest="analysis")
io_group.add_argument('-i',
"--config",
action="store",
help="Input config file",
dest="config")
io_group.add_argument('-j',
"--json",
action="store",
help="GISAID JSON data",
dest="json")
io_group.add_argument('-m',
"--metadata",
action="store",
help="Input metadata",
dest="metadata")
io_group.add_argument(
'--outdir',
action="store",
help="Output directory. Default: current working directory")
io_group.add_argument('-o',
'--output-prefix',
action="store",
help="Output prefix. Default: grinch",
dest="output_prefix")
io_group.add_argument("--alias", action="store", help="Alias JSON file")
io_group.add_argument('--filename', action="store", help="File to access.")
io_group.add_argument('--url', action="store", help="URL to access.")
io_group.add_argument('--username',
action="store",
help="Username for access.")
io_group.add_argument('--password',
action="store",
help="Password for access.")
misc_group = parser.add_argument_group('misc options')
misc_group.add_argument(
'--tempdir',
action="store",
help="Specify where you want the temporary stuff to go Default: $TMPDIR"
)
misc_group.add_argument("--no-temp",
action="store_true",
help="Output all intermediate files")
misc_group.add_argument("--verbose",
action="store_true",
help="Print lots of stuff to screen")
misc_group.add_argument("--no-force",
action="store_true",
help="Dont force run rules",
dest="no_force")
misc_group.add_argument('-t',
'--threads',
action='store',
dest="threads",
type=int,
help="Number of threads")
misc_group.add_argument("-v",
"--version",
action='version',
version=f"grinch {__version__}")
"""
Exit with help menu if no args supplied
"""
if len(sysargs) < 1:
parser.print_help()
sys.exit(-1)
else:
args = parser.parse_args(sysargs)
"""
Initialising dicts
"""
# get the default values from grinchfunks
config = gfunk.get_defaults()
data_install_checks.check_install(config)
dependency_checks.set_up_verbosity(config)
"""
Valid inputs are config.yaml/config.yml
"""
# find config file
if args.config:
gfunk.add_arg_to_config("config", args.config, config)
# if a yaml file is detected, add everything in it to the config dict
if config["config"]:
gfunk.parse_yaml_file(config["config"], config)
gfunk.add_arg_to_config("analysis", args.analysis, config)
gfunk.add_arg_to_config("metadata", args.metadata, config)
if config["analysis"] not in ["full", "report_only"]:
sys.stderr.write(
cyan(
f'Error: please speficify either `full` or `report_only` for analysis option.\n'
))
sys.exit(-1)
elif config["analysis"] == "full":
snakefile = data_install_checks.get_snakefile(thisdir)
else:
if not config["metadata"]:
sys.stderr.write(
cyan(
f'Error: please provide `metadata` for `report_only` grinch.\n'
))
sys.exit(-1)
snakefile = data_install_checks.get_report_snakefile(thisdir)
gfunk.add_arg_to_config("alias", args.alias, config)
config["flight_data_path"] = os.path.join(thisdir, "data", "flights")
config["import_report_path"] = os.path.join(thisdir, "data")
"""
Output directory
"""
# default output dir
gfunk.add_arg_to_config("outdir", args.outdir, config)
config["outdir"] = os.path.abspath(config["outdir"])
if not os.path.exists(config["outdir"]):
os.mkdir(config["outdir"])
figdir = os.path.join(config["outdir"], "figures")
if not os.path.exists(figdir):
os.mkdir(figdir)
config['figdir'] = figdir
"""
Get tempdir
"""
# specifying temp directory, outdir if no_temp (tempdir becomes working dir)
tempdir = gfunk.get_temp_dir(args.tempdir, args.no_temp, os.getcwd(),
config)
config["tempdir"] = tempdir
config["lineages_of_concern"] = [
"B.1.1.7", "B.1.351", "P.1", "B.1.617.2", "B.1.1.529"
]
config["snps"] = gfunk.get_snps()
"""
Miscellaneous options parsing
"""
# don't run in quiet mode if verbose specified
gfunk.add_arg_to_config("verbose", args.verbose, config)
gfunk.set_up_verbosity(config)
if args.no_force:
force_option = False
else:
force_option = True
config["force"] = force_option
gfunk.add_arg_to_config("threads", args.threads, config)
try:
config["threads"] = int(config["threads"])
except:
sys.stderr.write(
gfunk.cyan(
'Error: Please specifiy an integer for variable `threads`.\n'))
sys.exit(-1)
threads = config["threads"]
data_install_checks.check_access(args.json, args.username,
args.password, args.url, args.filename,
os.getcwd(), config)
if config["json"]:
pass
elif config["analysis"] == "full":
fn = config["filename"]
fn_unzipped = ".".join(fn.split(".")[:-1])
if os.path.exists(fn):
os.system(f"rm {fn}")
if os.path.exists(fn_unzipped):
os.system(f"rm {fn_unzipped}")
os.system(f"wget --password {config['password']} "
f"--user {config['username']} {config['url']} "
"&& "
f"bzip2 -d {fn} ")
config["json"] = os.path.join(os.getcwd(), fn_unzipped)
elif config["analysis"] == "report_only":
if not config["metadata"]:
sys.stderr.write(gfunk.cyan('Error: provide a metadata file.\n'))
sys.exit(-1)
# config["timestamp"] = gfunk.get_timestamp()
if config['verbose']:
print(green("\n**** CONFIG ****"))
for k in sorted(config):
print(green(k), config[k])
status = snakemake.snakemake(snakefile,
printshellcmds=True,
forceall=True,
force_incomplete=True,
workdir=tempdir,
config=config,
cores=threads,
lock=False)
else:
logger = custom_logger.Logger()
status = snakemake.snakemake(snakefile,
printshellcmds=False,
forceall=True,
force_incomplete=True,
workdir=tempdir,
config=config,
cores=threads,
lock=False,
quiet=True,
log_handler=config["log_api"])
if status: # translate "success" into shell exit code of 0
return 0
return 1