def get_argument_parser():
ap = get_default_argparser_with_base_opts(get_version(),
"Toolkit for cDNA analysis.",
default_level="WARN")
subparsers = ap.add_subparsers(dest="subCommand")
arg_parser = subparsers.add_parser(
'classify',
description="Classify reads based on whether they are " +
"non-chimeric, full length and have their 5', " +
"3' and poly A tail seen.")
# Add arguments for subcommand classify
add_classify_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'cluster',
description='Discover consensus isoforms based on ' +
'quality controlled non-chimeric, ' +
'full length reads to reference genome.')
# Add arguments for subcommand cluster
add_cluster_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'subset', description='Subset annotated reads in FASTA format.')
add_subset_arguments(_wrap_parser(arg_parser))
ap.add_argument("--profile",
action="store_true",
help="Print runtime profile at exit")
return ap
def get_argument_parser():
ap = get_default_argparser_with_base_opts(get_version(),
"Toolkit for cDNA analysis.", default_level="WARN")
subparsers = ap.add_subparsers(dest="subCommand")
arg_parser = subparsers.add_parser(
'classify',
description="Classify reads based on whether they are " +
"non-chimeric, full length and have their 5', " +
"3' and poly A tail seen.")
# Add arguments for subcommand classify
add_classify_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'cluster',
description='Discover consensus isoforms based on ' +
'quality controlled non-chimeric, ' +
'full length reads to reference genome.')
# Add arguments for subcommand cluster
add_cluster_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'subset',
description='Subset annotated reads in FASTA format.')
add_subset_arguments(_wrap_parser(arg_parser))
ap.add_argument(
"--profile", action="store_true",
help="Print runtime profile at exit")
return ap
class Constants(object):
"""Constants used in pbtranscript.tasks.gather_gmap_sam"""
TOOL_ID = "pbtranscript.tasks.gather_gmap_sam"
VERSION = get_version()
DRIVER = "python -m %s --resolved-tool-contract " % TOOL_ID
PARSER_DESC = __doc__
CHUNK_KEY = "$chunk.sam_id"
def get_parser():
"""Returns arg parser."""
parser = argparse.ArgumentParser(prog='tofu_wrap')
helpstr = "Input full-length non-chimeric reads in FASTA or ContigSet format " + \
"(e.g., isoseq_flnc.fasta|contigset.xml)"
parser.add_argument("flnc_fa", type=str, help=helpstr)
helpstr = "Output collapsed filtered isoforms in FASTA/FASTQ format (e.g., tofu_out.fastq)"
parser.add_argument("collapsed_filtered_fn", type=str, help=helpstr)
parser = add_nfl_fa_argument(parser, positional=False, required=True)
parser.add_argument("--nfl_reads_per_split", type=int,
dest="nfl_reads_per_split", default=60000,
help="Number of nFL reads per split file (default: 60000)")
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True, fasta_fofn=True)
# tofu output arguments
parser = add_tofu_output_arguments(parser)
parser = add_ice_arguments(parser) # Add Ice options, including --quiver
parser = add_sge_arguments(parser, blasr_nproc=True, quiver_nproc=True, gcon_nproc=True) # Sge
parser = add_ice_post_quiver_hq_lq_qv_arguments(parser) # IceQuiver HQ/LQ QV options.
parser = add_separate_flnc_arguments(parser) # separate_flnc options
parser = add_gmap_arguments(parser) # map to gmap reference options
parser = add_post_mapping_to_genome_arguments(parser) # post mapping to genome options
misc_group = parser.add_argument_group("Misc arguments")
misc_group.add_argument("--mem_debug", default=False, action="store_true",
help=argparse.SUPPRESS)
misc_group.add_argument("--keep_tmp_files", default=False, action="store_true",
help="False: delete tmp files; True: keep tmp files (default: False).")
misc_group.add_argument("--version", action='version', version='%(prog)s ' + str(get_version()))
return parser
def get_parser():
"""Returns arg parser."""
parser = argparse.ArgumentParser(prog='tofu_wrap')
helpstr = "Input full-length non-chimeric reads in FASTA or ContigSet format " + \
"(e.g., isoseq_flnc.fasta|contigset.xml)"
parser.add_argument("flnc_fa", type=str, help=helpstr)
helpstr = "Output collapsed filtered isoforms in FASTA/FASTQ format (e.g., tofu_out.fastq)"
parser.add_argument("collapsed_filtered_fn", type=str, help=helpstr)
parser = add_nfl_fa_argument(parser, positional=False, required=True)
parser.add_argument("--nfl_reads_per_split", type=int,
dest="nfl_reads_per_split", default=60000,
help="Number of nFL reads per split file (default: 60000)")
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True, fasta_fofn=True)
# tofu output arguments
parser = add_tofu_output_arguments(parser)
parser = add_ice_arguments(parser) # Add Ice options, including --quiver
parser = add_sge_arguments(parser, blasr_nproc=True, quiver_nproc=True, gcon_nproc=True) # Sge
parser = add_ice_post_quiver_hq_lq_qv_arguments(parser) # IceQuiver HQ/LQ QV options.
parser = add_separate_flnc_arguments(parser) # separate_flnc options
parser = add_gmap_arguments(parser) # map to gmap reference options
parser = add_post_mapping_to_genome_arguments(parser) # post mapping to genome options
misc_group = parser.add_argument_group("Misc arguments")
misc_group.add_argument("--mem_debug", default=False, action="store_true",
help=argparse.SUPPRESS)
misc_group.add_argument("--keep_tmp_files", default=False, action="store_true",
help="False: delete tmp files; True: keep tmp files (default: False).")
misc_group.add_argument("--version", action='version', version='%(prog)s ' + str(get_version()))
return parser
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,
ccs_fofn=args.ccs_fofn,
tmp_dir=args.tmp_dir)
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,
ccs_fofn=args.ccs_fofn,
done_filename=args.done_filename,
blasr_nproc=args.blasr_nproc,
tmp_dir=args.tmp_dir)
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,
tmp_dir=args.tmp_dir)
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 get_base_contract_parser(Constants=BaseConstants, default_level="WARN"):
p = get_pbparser(tool_id=Constants.TOOL_ID,
version=get_version(),
name=Constants.TOOL_ID,
description=Constants.PARSER_DESC,
driver_exe=Constants.DRIVER_EXE,
nproc=SymbolTypes.MAX_NPROC,
resource_types=(ResourceTypes.TMP_DIR, ),
default_level=default_level)
return p
def get_base_contract_parser(Constants=BaseConstants, default_level="WARN"):
p = get_pbparser(
tool_id=Constants.TOOL_ID,
version=get_version(),
name=Constants.TOOL_ID,
description=Constants.PARSER_DESC,
driver_exe=Constants.DRIVER_EXE,
nproc=SymbolTypes.MAX_NPROC,
resource_types=(ResourceTypes.TMP_DIR,),
default_level=default_level)
return p
def run(self):
"""Execute ice_partial.py all|one|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,
ccs_fofn=args.ccs_fofn,
tmp_dir=args.tmp_dir)
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,
ccs_fofn=args.ccs_fofn,
done_filename=args.done_filename,
blasr_nproc=args.blasr_nproc,
tmp_dir=args.tmp_dir)
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,
tmp_dir=args.tmp_dir)
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 main():
"""Main function, split a fasta into smaller chunks."""
import logging
from pbtranscript.__init__ import get_version
log = logging.getLogger(__name__)
args = get_args()
from pbtranscript.Utils import setup_log
setup_log(alog=log, level=logging.DEBUG)
log.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
splitFasta(input_fasta=args.input_fasta,
reads_per_split=args.reads_per_split,
out_dir=args.out_dir,
out_prefix=args.out_prefix)
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
args = self.args
try:
convert_fofn_to_fasta(fofn_filename=args.input_fofn,
out_filename=args.fasta_fofn,
fasta_out_dir=args.fasta_out_dir,
force_overwrite=False)
except:
logging.exception("Failed to convert fofn {f} to fasta.".format(
f=args.input_fofn))
return 1
return 0
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
args = self.args
try:
convert_fofn_to_fasta(fofn_filename=args.input_fofn,
out_filename=args.fasta_fofn,
fasta_out_dir=args.fasta_out_dir,
force_overwrite=False)
except:
logging.exception("Failed to convert fofn {f} to fasta.".
format(f=args.input_fofn))
return 1
return 0
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
iceqm = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
cmd_str = iceqm.cmd_str()
iceqm.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".
format(cmd_str=cmd_str))
return 1
return 0
def main():
"""Main function, split a fasta into smaller chunks."""
import logging
from pbtranscript.__init__ import get_version
log = logging.getLogger(__name__)
args = get_args()
from pbtranscript.Utils import setup_log
setup_log(alog=log, level=logging.DEBUG)
log.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
splitFasta(input_fasta=args.input_fasta,
reads_per_split=args.reads_per_split,
out_dir=args.out_dir,
out_prefix=args.out_prefix)
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
iceqm = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
cmd_str = iceqm.cmd_str()
iceqm.run()
except:
logging.exception("Exiting {cmd_str} with return code 1.".
format(cmd_str=cmd_str))
return 1
return 0
def set_parser():
"""Set up and return argument parser."""
parser = ArgumentParser()
parser.add_argument("input_fasta",
help="Input fasta filename")
parser.add_argument("output_prefix",
help="Output filename prefix (ex: g_consensus)")
parser.add_argument("consensus_id",
help="Consensus sequence ID name (ex: consensus)")
parser.add_argument("--nproc",
default=8, type=int,
help="Number of processes")
parser.add_argument("--maxScore", default=-1000, type=int,
help="blasr maxScore")
parser.add_argument("--version", "-v",
action='version', version='%(prog)s ' + get_version())
return parser
def set_parser():
"""Set up and return argument parser."""
parser = ArgumentParser()
parser.add_argument("input_fasta", help="Input fasta filename")
parser.add_argument("output_prefix",
help="Output filename prefix (ex: g_consensus)")
parser.add_argument("consensus_id",
help="Consensus sequence ID name (ex: consensus)")
parser.add_argument("--nproc",
default=8,
type=int,
help="Number of processes")
parser.add_argument("--maxScore",
default=-1000,
type=int,
help="blasr maxScore")
parser.add_argument("--version",
"-v",
action='version',
version='%(prog)s ' + get_version())
return parser
def run(self):
"""Execute ice_fa2fq.py."""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=get_version()))
cmd_str = ""
try:
args = self.args
in_fa, ccs_fofn, out_fq = args.in_fa, args.ccs_fofn, \
args.out_fq
self.validate_inputs(in_fa=in_fa, ccs_fofn=ccs_fofn)
cmd_str = self.cmd_str(in_fa=in_fa,
ccs_fofn=ccs_fofn,
out_fq=out_fq)
ice_fa2fq(in_fa=in_fa, ccs_fofn=ccs_fofn, out_fq=out_fq)
except:
logging.exception(
"Exiting {cmd} with return code 1.".format(cmd=cmd_str))
return 1
return 0
def _logConfigs(self):
"""Log configuration."""
with open(self.configFN, 'w', 0) as f:
f.write('pbtranscript ' + get_version() + "\n")
f.write(str(self.ice_opts) + "\n")
f.write(str(self.sge_opts) + "\n")
def getVersion(self):
"""Return version string."""
return get_version()
def getVersion(self):
return get_version()
def run(self):
"""Execute ice_quiver.py all|i|merge|postprocess."""
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 = SgeOptions2(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
blasr_nproc=args.blasr_nproc,
arrow_nproc=args.arrow_nproc,
sge_env_name=args.sge_env_name,
sge_queue=args.sge_queue,
qsub_extra=args.qsub_extra)
ipq_opts = IceArrowHQLQOptions2(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_arrow_min_accuracy=args.hq_arrow_min_accuracy)
obj = IceArrowAll2(root_dir=args.root_dir,
subread_xml=args.subread_xml,
sge_opts=sge_opts,
ipq_opts=ipq_opts,
tmp_dir=args.tmp_dir)
# elif cmd == "i":
# 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,
# arrow_nproc=args.arrow_nproc)
# obj = IceQuiverI(root_dir=args.root_dir, i=args.i, N=args.N,
# bas_fofn=args.bas_fofn,
# fasta_fofn=None,
# sge_opts=sge_opts,
# tmp_dir=args.tmp_dir)
#elif cmd == "merge":
# obj = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
elif cmd == "postprocess":
ipq_opts = IceArrowHQLQOptions2(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_arrow_min_accuracy=args.hq_arrow_min_accuracy,
hq_min_full_length_reads=args.hq_min_full_length_reads)
obj = IceArrowPostProcess2(
root_dir=args.root_dir,
ipq_opts=ipq_opts,
quit_if_not_done=args.quit_if_not_done,
summary_fn=args.summary_fn,
report_fn=args.report_fn)
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|one|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 in ('all', 'one'):
# currently user NOT allowed to set full missed start/end
# (we also set it to 30/10 bp which is more stringent than in IceIterative2,
# which is hard set to 50/30)
ice_opts = IceOptions2(ece_penalty=args.ece_penalty,
ece_min_len=args.ece_min_len,
max_missed_start=args.max_missed_start,
max_missed_end=args.max_missed_end,
full_missed_start=30,
full_missed_end=10,
min_match_len=50,
aligner_choice=args.aligner_choice)
if cmd == "all":
sge_opts = SgeOptions2(unique_id=args.unique_id,
use_sge=args.use_sge,
max_sge_jobs=args.max_sge_jobs,
sge_queue=args.sge_queue,
sge_env_name=args.sge_env_name,
qsub_extra=args.qsub_extra)
obj = IceAllPartials2(
root_dir=args.root_dir,
fasta_filenames=args.fasta_filenames.split(','),
fastq_filenames=args.fastq_filenames.split(',')
if args.fastq_filenames is not None else None,
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
ice_opts=ice_opts,
sge_opts=sge_opts,
cpus=args.cpus,
tmp_dir=args.tmp_dir)
elif cmd == "one":
# Only assign nfl reads in the given input_fasta file to isoforms
# "one" is always run locally so no need for SGE option
obj = IcePartialOne2(input_fasta=args.input_fasta,
input_fastq=args.input_fastq,
ref_fasta=args.ref_fasta,
out_pickle=args.out_pickle,
done_filename=args.done_filename,
ice_opts=ice_opts,
cpus=args.cpus,
tmp_dir=args.tmp_dir)
elif cmd == "split":
obj = IcePartialSplit2(root_dir=args.root_dir,
nfl_fa=args.nfl_fa,
nfl_fq=args.nfl_fq,
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,
# tmp_dir=args.tmp_dir)
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_quiver.py all|i|merge|postprocess."""
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,
quiver_nproc=args.quiver_nproc)
ipq_opts = IceQuiverHQLQOptions(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy)
obj = IceQuiverAll(root_dir=args.root_dir,
bas_fofn=args.bas_fofn,
fasta_fofn=None,
sge_opts=sge_opts,
ipq_opts=ipq_opts,
tmp_dir=args.tmp_dir)
elif cmd == "i":
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,
quiver_nproc=args.quiver_nproc)
obj = IceQuiverI(root_dir=args.root_dir, i=args.i, N=args.N,
bas_fofn=args.bas_fofn,
fasta_fofn=None,
sge_opts=sge_opts,
tmp_dir=args.tmp_dir)
elif cmd == "merge":
obj = IceQuiverMerge(root_dir=args.root_dir, N=args.N)
elif cmd == "postprocess":
ipq_opts = IceQuiverHQLQOptions(
hq_isoforms_fa=args.hq_isoforms_fa,
hq_isoforms_fq=args.hq_isoforms_fq,
lq_isoforms_fa=args.lq_isoforms_fa,
lq_isoforms_fq=args.lq_isoforms_fq,
qv_trim_5=args.qv_trim_5,
qv_trim_3=args.qv_trim_3,
hq_quiver_min_accuracy=args.hq_quiver_min_accuracy)
obj = IceQuiverPostprocess(root_dir=args.root_dir,
ipq_opts=ipq_opts,
use_sge=args.use_sge,
quit_if_not_done=args.quit_if_not_done,
summary_fn=args.summary_fn,
report_fn=args.report_fn)
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