def __init__(self, **kwargs):
self.job_type = 'jsonmerger'
ExternalSeppJob.__init__(self, self.job_type, **kwargs)
self.out_file = None
self.distribution = False
self.taxonomy = None
self.mapping = None
self.threshold = None
self.classification_file = None
self.elim = float(options().hmmsearch.elim)
if options().hmmsearch.filters.upper() == "TRUE":
self.filters = True
else:
if options().hmmsearch.filters.upper() == "FALSE":
self.filters = False
else:
self.filters = None
if self.filters is None:
raise Exception(
"Expecting true/false for options().hmmsearch.filters")
self.strategy = options().exhaustive.strategy
self.minsubsetsize = int(options().exhaustive.minsubsetsize)
self.alignment_threshold = float(options().alignment_threshold)
self.molecule = options().molecule
self.placer = options().exhaustive.__dict__['placer'].lower()
self.cutoff = 0
def __init__(self, pipe=0, **kwargs):
self.pipe = pipe
if pipe == 0:
'''By default errors and output is piped to this process.
output/err will be available at as self.stdoutdata and
self.stderrdata and also will be logged'''
pass
elif pipe == 1:
'''The following line forces output to be saved to a file. Note
that
1- A file object/descriptor cannot be used here because this is
executed in parent process, and in child process those file
handlers will not be available.
2- self.stdoutdata and self.stderrdata will not be automatically
filled (to avoid unnecessary I/O). Read stderr and stdout in
read_results if necessary.
'''
kwargs['stdout'] = "./.stdout"
kwargs['stderr'] = "./.stderr"
'''always call parent constructor'''
ExternalSeppJob.__init__(self, "test_find_job", path='dummy', **kwargs)
'''inputs that need to be set before running this job'''
self.pattern = None
self.options = None
def __init__(self, **kwargs):
self.job_type = 'jsonmerger'
ExternalSeppJob.__init__(self, self.job_type, **kwargs)
self.out_file = None
self.distribution = False
self.taxonomy = None
self.mapping = None
self.threshold = None
self.classification_file = None
self.elim = float(options().hmmsearch.elim)
if options().hmmsearch.filters.upper() == "TRUE":
self.filters = True
else:
if options().hmmsearch.filters.upper() == "FALSE":
self.filters = False
else:
self.filters = None
if self.filters is None:
raise Exception(
"Expecting true/false for options().hmmsearch.filters")
self.strategy = options().exhaustive.strategy
self.minsubsetsize = int(options().exhaustive.minsubsetsize)
self.alignment_threshold = float(options().alignment_threshold)
self.molecule = options().molecule
self.placer = options().exhaustive.__dict__['placer'].lower()
self.cutoff = 0
def __init__(self, pipe = 0, **kwargs):
self.pipe = pipe
if pipe == 0:
'''By default errors and output is piped to this process.
output/err will be available at as self.stdoutdata and self.stderrdata
and also will be logged'''
pass
elif pipe == 1:
'''The following line forces output to be saved to a file. Note that
1- A file object/descriptor cannot be used here because this is
executed in parent process, and in child process those file handlers
will not be available.
2- self.stdoutdata and self.stderrdata will not be automatically
filled (to avoid unnecessary I/O). Read stderr and stdout in
read_results if necessary.
'''
kwargs['stdout'] = "./.stdout"
kwargs['stderr'] = "./.stderr"
'''always call parent constructor'''
ExternalSeppJob.__init__(self, "test_find_job", **kwargs)
'''inputs that need to be set before running this job'''
self.pattern = None
self.options = None