def __init__(self, fastqInput1=None, fastqInput2=None, ht2Idx=None, samOutputDir=None, threads=None, cmdParam=None, **kwargs): super(Step, self).__init__(cmdParam, **kwargs) # set all input and output parameters #self.setParamIO('fastqInput1',fastqInput1) self.setParamIO('fastqInput1', fastqInput1) self.setParamIO('fastqInput2', fastqInput2) self.setParamIO('ht2Idx', ht2Idx) self.setParamIO('samOutputDir', samOutputDir) # call self.initIO() self.initIO() #set other parameters #self.setParam('isNoDiscordant', isNoDiscordant) if threads is None: self.setParam('threads', Configure.getThreads()) else: self.setParam('threads', threads)
def __init__(self, fastqInput=None, fileFormat=None, fastqcOutputDir=None, threads=None, cmdParam=None, **kwargs): super(Step, self).__init__(cmdParam, **kwargs) # set all input and output parameters self.setParamIO('fastqInput', fastqInput) if fastqcOutputDir == None: self.setParamIO('fastqcOutputDir', Configure.getTmpDir()) else: self.setParamIO('fastqcOutputDir', fastqcOutputDir) # call self.initIO() self.initIO() #set other parameters #self.setParam('isNoDiscordant', isNoDiscordant) self.setParam('fileFormat', fileFormat) if threads is None: threads = Configure.getThreads() self.setParam('threads', threads) print(self.params)
def __init__(self, bamInput = None, gtfInput = None, outputDir = None, threads = None, ismultiReadCorrect = None, isupperQuartileForm = None, istotalHitsNorm = True, fragLenMean = 200, fragLenStdDev = 80, cmdParam = None, **kwargs ): super(Step, self).__init__(cmdParam,**kwargs) self.setParamIO('bamInput',bamInput) self.setParamIO('gtfInput',gtfInput) self.setParamIO('outputDir',outputDir) #self.setParamIO('fragBiasCorrectInput',fragBiasCorrectInput) self.initIO() self.setParam('ismultiReadCorrect',ismultiReadCorrect) self.setParam('fragLenMean',fragLenMean) self.setParam('fragLenStdDev',fragLenStdDev) self.setParam('isupperQuartileForm',isupperQuartileForm) self.setParam('istotalHitsNorm',istotalHitsNorm) if threads is None: threads = Configure.getThreads() self.setParam('threads',threads)
def __init__(self, fastqInput1=None, fastqInput2=None, fastqOutputDir1=None, fastqOutputDir2=None, adapter1=None, adapter2=None, threads=None, cmdParamFindAdapter=None, cmdParam=None, **kwargs): super(Step, self).__init__(cmdParam=[cmdParamFindAdapter, cmdParam], **kwargs) """ called by 'AdapterRemoval()' __init__(): Initialize the class with inputs, outputs and other parameters. Setting all parameter is the main target of this function. """ # set all input and output parameters self.setParamIO('fastqInput1', fastqInput1) self.setParamIO('fastqInput2', fastqInput2) self.setParamIO('fastqOutputDir1', fastqOutputDir1) self.setParamIO('fastqOutputDir2', fastqOutputDir2) # call self.initIO() self.initIO() #set other parameters if threads is None: threads = Configure.getThreads() self.setParam('threads', threads) if adapter1 is None: self.setParam('adapter1', None) elif len(adapter1) > 1: self.setParam('adapter1', adapter1) elif os.path.exists(adapter1): self.setParam('adapter1', self.getListInFile()) else: self.setParam('adapter1', adapter1) if adapter2 is None: self.setParam('adapter2', None) elif len(adapter1) > 1: self.setParam('adapter2', adapter2) elif os.path.exists(adapter2): self.setParam('adapter2', self.getListInFile()) else: self.setParam('adapter2', adapter2) self.adapter1 = {} self.adapter2 = {}
def __init__(self, faInput1=None, gtfInput1=None, assembliesInput=None, threads=None, gtfOutputDir=None, cmdParam=None, **kwargs): super(Step, self).__init__(cmdParam, **kwargs) self.setParamIO('faInput1', faInput1) self.setParamIO('gtfInput1', gtfInput1) self.setParamIO('assembliesInput', assembliesInput) self.setParamIO('gtfOutputDir', gtfOutputDir) self.initIO() if threads is None: threads = Configure.getThreads() self.setParam('threads', threads)
def __init__(self, fastqInput = None, outFileDir = None, genomeDir = None, threads = None, #outSamType = 'BAM' cmdParam = None, **kwargs): super(Step, self).__init__(cmdParam, ** kwargs) self.setParamIO('fastqInput', fastqInput) self.setParamIO('outFileDir', outFileDir) self.setParamIO('genomeDir', genomeDir) self.initIO() #self.setParam('outSamType', outSamType) if threads is None: threads = Configure.getThreads() self.setParam('threads', threads)
def __init__(self, fastqInput1=None, fastqInput2=None, bt2Idx=None, samOutputDir=None, mapRsOutputDir=None, threads=None, isNoDiscordant=True, isNoUnal=True, isNoMixed=True, X=2000, cmdParam=None, **kwargs): super(Step, self).__init__(cmdParam, **kwargs) """ called by 'Bowtie()' __init__(): Initialize the class with inputs, outputs and other parameters. Setting all parameter is the main target of this function. """ # set all input and output parameters self.setParamIO('fastqInput1', fastqInput1) self.setParamIO('fastqInput2', fastqInput2) self.setParamIO('bt2Idx', bt2Idx) self.setParamIO('samOutputDir', samOutputDir) self.setParamIO('mapRsOutputDir', mapRsOutputDir) # call self.initIO() self.initIO() #set other parameters self.setParam('isNoDiscordant', isNoDiscordant) self.setParam('isNoUnal', isNoUnal) self.setParam('isNoMixed', isNoMixed) self.setParam('X', X) if threads is None: threads = Configure.getThreads() self.setParam('threads', threads)