Esempio n. 1
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 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
Esempio n. 2
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    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
Esempio n. 3
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 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