def __init__(self, analysis, suffix="", readFilter='all', strand='Plus'):
self.suffix = str(suffix)
self.readFilter = readFilter
self.strand = strand
LogicalStep.__init__(self, analysis, 'bamToBws_' + \
readFilter.lower() + strand + '_' + suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix="", readFilter='all', strand='Plus'):
self.suffix = str(suffix)
self.readFilter = readFilter
self.strand = strand
LogicalStep.__init__(self, analysis, 'bamToBws_' + \
readFilter.lower() + strand + '_' + suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, replicate='1', libId='', encoding='sanger', tagLen=100):
self.replicate = str(replicate)
self.encoding = encoding
self.libId = libId
self.tagLen = int(tagLen)
LogicalStep.__init__(self, analysis, 'alignmentByTophat_' + analysis.readType + 'Rep' + \
self.replicate)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all step versions
def __init__(self, analysis, suffix='', expType='ChIPseq',isPaired=False):
self.suffix = str(suffix)
self.expType = str(expType)
self.isPaired = isPaired
LogicalStep.__init__(self, analysis, 'peaksByMacs_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, replicate1='1', replicate2='2'):
self.replicate1 = str(replicate1)
self.replicate2 = str(replicate2)
LogicalStep.__init__(self, analysis, \
'mergeBam_Rep' + self.replicate1 + 'Rep' + self.replicate2)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix='', tagLen=50):
self.suffix = str(suffix)
self.tagLen = int(tagLen)
LogicalStep.__init__(self, analysis, 'peaksByHotspot_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, replicate="1", suffix=""):
self.replicate = str(replicate)
self.suffix = suffix
LogicalStep.__init__(self, analysis, 'bamEvaluate' + self.suffix)
def __init__(self, analysis, replicate="1", encoding='sanger'):
self.replicate = str(replicate)
self.encoding = encoding
LogicalStep.__init__(self, analysis, 'alignmentByBwa_' + analysis.readType + 'Rep' + \
self.replicate)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all step versions
def __init__(self, analysis, suffix=''):
self.suffix = str(suffix)
LogicalStep.__init__(self, analysis, 'fastqValidation_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix='', expType='ChIPseq', isPaired=False):
self.suffix = str(suffix)
self.expType = str(expType)
self.isPaired = isPaired
LogicalStep.__init__(self, analysis, 'peaksByMacs_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix=''):
self.suffix = str(suffix)
LogicalStep.__init__(self, analysis, 'fastqValidation_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix='', tagLen=50):
self.suffix = str(suffix)
self.tagLen = int(tagLen)
LogicalStep.__init__(self, analysis, 'peaksByHotspot_' + self.suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
def __init__(self, analysis, suffix=""):
self.suffix = str(suffix)
LogicalStep.__init__(self, analysis, 'quantitateRsem_' + analysis.readType + '_' + suffix)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all step versions
def __init__(self, analysis, replicate1="1", replicate2="2"):
self.replicate1 = str(replicate1)
self.replicate2 = str(replicate2)
LogicalStep.__init__(self, analysis, "mergeBam_Rep" + self.replicate1 + "Rep" + self.replicate2)
self._stepVersion = self._stepVersion + 0 # Increment allows changing all set versions
