def run(self):
"""Execute ice_partial.py all|split|i|merge."""
cmd = self.args.subCommand
logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__),
cmd=cmd,
v=get_version()))
cmd_str = ""
try:
args = self.args
obj = None
if cmd == "all":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc)
obj = IceAllPartials(
root_dir=args.root_dir,
fasta_filenames=args.fasta_filenames.split(','),
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sge_opts=sge_opts,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn)
elif cmd == "one":
# Only assign nfl reads in the given input_fasta file to isoforms
obj = IcePartialOne(input_fasta=args.input_fasta,
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn,
done_filename=args.done_filename,
blasr_nproc=args.blasr_nproc,
use_finer_qv=args.use_finer_qv)
elif cmd == "split":
obj = IcePartialSplit(root_dir=args.root_dir,
nfl_fa=args.nfl_fa,
N=args.N)
elif cmd == "i":
obj = IcePartialI(root_dir=args.root_dir,
i=args.i,
ccs_fofn=args.ccs_fofn,
blasr_nproc=args.blasr_nproc)
elif cmd == "merge":
obj = IcePartialMerge(root_dir=args.root_dir, N=args.N)
else:
raise ValueError(
"Unknown command passed to {f}: {cmd}.".format(
f=op.basename(__file__), cmd=cmd))
cmd_str = obj.cmd_str()
logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str))
obj.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".format(
cmd_str=cmd_str))
return 1
return 0
def run(self):
"""Execute ice_partial.py all|split|i|merge."""
cmd = self.args.subCommand
logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__),
cmd=cmd, v=get_version()))
cmd_str = ""
try:
args = self.args
obj = None
if cmd == "all":
sge_opts = SgeOptions(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc)
obj = IceAllPartials(root_dir=args.root_dir,
fasta_filenames=args.fasta_filenames.split(','),
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sge_opts=sge_opts,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn)
elif cmd == "one":
# Only assign nfl reads in the given input_fastq file to isoforms
obj = IcePartialOne(input_fastq=args.input_fastq,
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
sa_file=args.sa_file,
ccs_fofn=args.ccs_fofn,
done_filename=args.done_filename,
blasr_nproc=args.blasr_nproc,
use_finer_qv=args.use_finer_qv)
elif cmd == "split":
obj = IcePartialSplit(root_dir=args.root_dir,
nfl_fa=args.nfl_fa,
N=args.N)
elif cmd == "i":
obj = IcePartialI(root_dir=args.root_dir, i=args.i,
ccs_fofn=args.ccs_fofn,
blasr_nproc=args.blasr_nproc)
elif cmd == "merge":
obj = IcePartialMerge(root_dir=args.root_dir,
N=args.N)
else:
raise ValueError("Unknown command passed to {f}: {cmd}.".
format(f=op.basename(__file__), cmd=cmd))
cmd_str = obj.cmd_str()
logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str))
obj.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".
format(cmd_str=cmd_str))
return 1
return 0
