def __init__(self, **keywords): """ """ AbstractMapper.__init__(self, **keywords) import re self.numberGrabPattern = re.compile(r"^(\d+) \+ (\d+)")
def __init__(self, inputFnameLs=None, **keywords): """ 2012.5.23 """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords) self.chromosomeList = utils.getListOutOfStr(self.chromosomeList, data_type=str, separator2=None) self.chromosomeSet = set(self.chromosomeList) self.fileFormatDict = {1: 'fasta', 2: 'fastq'} if not self.inputFileFormat: #0 or None or '' #use 1: to exclude the '.' in suffix self.inputFileFormat = utils.getRealPrefixSuffixOfFilenameWithVariableSuffix( self.inputFname)[1][1:] else: self.inputFileFormat = self.fileFormatDict.get( self.inputFileFormat) if not self.outputFileFormat: #0 or None or '' self.outputFileFormat = utils.getRealPrefixSuffixOfFilenameWithVariableSuffix( self.outputFname)[1][1:] else: self.outputFileFormat = self.fileFormatDict.get( self.outputFileFormat)
def __init__(self, inputFnameLs, **keywords): """ 2012.5.23 """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords) #self.blastnPath = self.insertHomePath(self.blastnPath, self.home_path) self.blastallPath = self.insertHomePath(self.blastallPath, self.home_path)
def __init__(self, **keywords): """ """ AbstractMapper.__init__(self, **keywords) self.convertFuncDict = { 1: self.convertMSOutput, 2: self.convertMSHOTLiteOutput }
def __init__(self, inputFnameLs=None, **keywords): """ 2012.10.25 self.missingDataNotation will be processed into a set. """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords) #self.connectDB() called within its __init__() #if user wants to preserve data in a data structure that is visible throughout reading different files. # then use this self.invariantPData. self.invariantPData = PassingData(writer=None, headerOutputted=False, x_ls = [], y_ls = [], z_ls=[]) if getattr(self, 'missingDataNotation', None): self.missingDataNotation = set(utils.getListOutOfStr(self.missingDataNotation, data_type=str, separator2=None)) else: self.missingDataNotation = set()
def __init__(self, inputFnameLs=None, **keywords): """ """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs, **keywords): """ """ AbstractMapper.__init__(self, **keywords) self.inputFnameLs = inputFnameLs #2012.3.19 not used
def __init__(self, **keywords): """ """ AbstractMapper.__init__(self, **keywords)
def __init__(self, inputFnameLs, **keywords): """ 2012.8.19 """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs=None, **keywords): AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, **keywords): """ """ AbstractMapper.__init__(self, **keywords) """
def __init__(self, inputFnameLs=None, **keywords): """ 2011-7-12 """ AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs, **keywords): """ """ AbstractMapper.__init__(self, **keywords) self.inputFnameLs = inputFnameLs #useless