def parse_input_file(cls, input_file, shifter):
# assumes lume-genesis can best installed locally - shifter execution not needed
# expand_paths is not used to ensure that generated input files are used if desired - otherwise rsopt symlinks them to run dir
import genesis
d = genesis.Genesis(input_file,
use_tempdir=False,
expand_paths=False,
check_executable=False)
return d
def __init__(self, address, cache=None,
username='******', password='******',
connect=True):
"""
:param str address: The address of the API.
:param str username:
:param str password: Login info; None for public access.
:param CacheSQLite cache: A cache that stores results locally (an
:obj:`CacheSQLite`).
"""
self.address = address
self.buffer = cache
self.username = username
self.password = password
self._gen = None
if connect:
self._gen = genesis.Genesis(username, password, address)
self._project = None
self.projectid = None
def gen(self):
if not self._gen:
self._gen = genesis.Genesis(self.username, self.password,
self.address)
return self._gen
'--email',
default='*****@*****.**',
help='Sign-in e-mail')
parser.add_argument('-p',
'--password',
default='anonymous',
help='Sign-in password')
parser.add_argument('-r', metavar='READS', help='NGS fastq file')
parser.add_argument('-r1', metavar='READS-1', help='NGS fastq file (mate 1)')
parser.add_argument('-r2', metavar='READS-2', help='NGS fastq file (mate 2)')
args = parser.parse_args()
if not (args.r or (args.r1 and args.r2)) or \
(args.r and (args.r1 or args.r2)):
parser.print_help()
print
print "ERROR: define either -r or -r1 and -r2."
print
exit(1)
g = genesis.Genesis(args.email, args.password, args.address)
if args.r:
r = g.upload(args.project, 'import:upload:reads-fastq', src=args.r)
else:
r = g.upload(args.project,
'import:upload:reads-fastq-paired-end',
src1=args.r1,
src2=args.r2)