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, '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