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)
Пример #3
0
    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)
Пример #4
0
    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)
Пример #9
0
	def __init__(self, inputFnameLs, **keywords):
		"""
		2012.8.19
		"""
		AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
Пример #10
0
 def __init__(self, inputFnameLs=None, **keywords):
     AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
	def __init__(self,  **keywords):
		"""
		"""
		AbstractMapper.__init__(self, **keywords)
		"""
Пример #12
0
    def __init__(self, inputFnameLs=None, **keywords):
        """
		2011-7-12
		"""
        AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
Пример #13
0
    def __init__(self, inputFnameLs, **keywords):
        """
		"""
        AbstractMapper.__init__(self, **keywords)
        self.inputFnameLs = inputFnameLs  #useless