def __init__(self,
args=None,
argumentList=(),
output_dataset_type=AlignmentSet):
"""Initialize a PBAlignRunner object.
argumentList is a list of arguments, such as:
['--debug', '--maxHits', '10', 'in.fasta', 'ref.fasta', 'out.sam']
"""
desc = "Utilities for aligning PacBio reads to reference sequences."
if args is None: # FIXME unit testing hack
args = get_contract_parser().arg_parser.parser.parse_args(
argumentList)
self.args = args
# args.verbosity is computed by counting # of 'v's in '-vv...'.
# However in parseOptions, arguments are parsed twice to import config
# options and then overwrite them with argumentList (e.g. command-line)
# options.
#self.args.verbosity = 1 if (self.args.verbosity is None) else \
# (int(self.args.verbosity) / 2 + 1)
super(PBAlignRunner, self).__init__(desc)
self._output_dataset_type = output_dataset_type
self._alnService = None
self._filterService = None
self.fileNames = PBAlignFiles()
self._tempFileManager = TempFileManager()
def run_rtc(rtc):
p = get_contract_parser().arg_parser.parser
argv = [
rtc.task.input_files[0], rtc.task.input_files[1],
rtc.task.output_files[0], "--nproc",
str(rtc.task.nproc), "--maxMatch", "15", "--algorithmOptions",
'--placeGapConsistently --scoreMatrix "-1 4 4 4 6 4 -1 4 4 6 4 4 -1 4 6 4 4 4 -1 6 6 6 6 6 6"',
"--tmpDir", rtc.task.tmpdir_resources[0].path, "--log-level",
rtc.task.log_level
]
return args_runner(args=p.parse_args(argv),
output_dataset_type=ConsensusAlignmentSet)
def run_rtc(rtc):
p = get_contract_parser().arg_parser.parser
argv = [
rtc.task.input_files[0],
rtc.task.input_files[1],
rtc.task.output_files[0],
"--nproc", str(rtc.task.nproc),
"--maxMatch", "15",
"--algorithmOptions",
'--placeGapConsistently --scoreMatrix "-1 4 4 4 6 4 -1 4 4 6 4 4 -1 4 6 4 4 4 -1 6 6 6 6 6 6"',
"--tmpDir", rtc.task.tmpdir_resources[0].path,
"--log-level", rtc.task.log_level
]
return args_runner(
args=p.parse_args(argv),
output_dataset_type=ConsensusAlignmentSet)
def __init__(self, args=None, argumentList=(),
output_dataset_type=AlignmentSet):
"""Initialize a PBAlignRunner object.
argumentList is a list of arguments, such as:
['--debug', '--maxHits', '10', 'in.fasta', 'ref.fasta', 'out.sam']
"""
desc = "Utilities for aligning PacBio reads to reference sequences."
if args is None: # FIXME unit testing hack
args = get_contract_parser().arg_parser.parser.parse_args(argumentList)
self.args = args
# args.verbosity is computed by counting # of 'v's in '-vv...'.
# However in parseOptions, arguments are parsed twice to import config
# options and then overwrite them with argumentList (e.g. command-line)
# options.
#self.args.verbosity = 1 if (self.args.verbosity is None) else \
# (int(self.args.verbosity) / 2 + 1)
super(PBAlignRunner, self).__init__(desc)
self._output_dataset_type = output_dataset_type
self._alnService = None
self._filterService = None
self.fileNames = PBAlignFiles()
self._tempFileManager = TempFileManager()