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)
