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=None, **keywords):
		"""
		"""
		parentClass.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		self.alignmentIDList = utils.getListOutOfStr(list_in_str=self.alignmentIDList, data_type=int)
		
		self.characterPattern = re.compile(r'[a-zA-Z]')
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		"""
		AbstractMatrixFileWalker.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		if hasattr(self, 'phenotypeIDList'):
			self.phenotypeIDList = utils.getListOutOfStr(self.phenotypeIDList)
		else:
			self.phenotypeIDList = None
	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()
Exemple #5
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    def __init__(self, inputFnameLs, **keywords):
        """
		2011-7-12
		"""
        ReduceMatrixByMergeColumnsWithSameKey.__init__(self, inputFnameLs,
                                                       **keywords)

        if self.valueColumnLs:
            self.valueColumnLs = utils.getListOutOfStr(self.valueColumnLs,
                                                       data_type=int)
        else:
            self.valueColumnLs = []
	def __init__(self,  **keywords):
		"""
		2012.9.17 call parentClass.__init__() directly
		2011-7-11
		"""
		self.pathToInsertHomePathList.extend(['sfs_code_path'])
		
		parentClass.__init__(self, **keywords)
		
		if hasattr(self, 'simulateLocusLengthList', None):
			self.simulateLocusLengthList = utils.getListOutOfStr(self.simulateLocusLengthList, data_type=int)
		else:
			self.simulateLocusLengthList = []
    def __init__(self, **keywords):
        """
		2012.9.17 call parentClass.__init__() directly
		2011-7-11
		"""
        self.pathToInsertHomePathList.extend(['sfs_code_path'])

        parentClass.__init__(self, **keywords)

        if hasattr(self, 'simulateLocusLengthList', None):
            self.simulateLocusLengthList = utils.getListOutOfStr(
                self.simulateLocusLengthList, data_type=int)
        else:
            self.simulateLocusLengthList = []
Exemple #8
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	def __init__(self, inputFnameLs=None, **keywords):
		"""
		2011-7-12
		"""
		AbstractReducer.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		if self.keyColumnLs:
			self.keyColumnLs = utils.getListOutOfStr(self.keyColumnLs, data_type=int)
		else:
			self.keyColumnLs = []
		if self.keyHeaderLs:
			self.keyHeaderLs = self.keyHeaderLs.split(',')
		else:
			self.keyHeaderLs = []
		
		self.keyColumnSet = set(self.keyColumnLs)
	def addObjectListAttributeToSet(self, attributeName=None, setVariable=None, data_type=None):
		"""
		2013.09.10 bugfix, added argument data_type
		2012.12.3
		2012.12.2 bugfix
		2012.11.23
		"""
		attributeValue = self.getAttribute(attributeName, None)
		flag = False
		if type(attributeValue)==numpy.ndarray:	#"if attributeValue" fails for numpy array
			if hasattr(attributeValue, '__len__') and attributeValue.size>0:
				flag = True
		elif attributeValue or attributeValue == 0:
			flag = True
		if flag and setVariable is not None:
			if type(attributeValue)==str:
				attributeValueList = getListOutOfStr(attributeValue, data_type=data_type, separator1=',', separator2='-')
			else:
				attributeValueList = attributeValue
			setVariable |= set(list(attributeValueList))
		return setVariable
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		"""
		AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		self.sequencedMonkeyCountryIDList = utils.getListOutOfStr(self.sequencedMonkeyCountryIDList)
		self.newSampleMonkeyCountryIDList = utils.getListOutOfStr(self.newSampleMonkeyCountryIDList)
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		"""
		parentClass.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		self.perturbedMonkeyList = utils.getListOutOfStr(list_in_str=self.perturbedMonkeyList, data_type=str, separator1=',', separator2=None)
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		"""
		parentClass.__init__(self, inputFnameLs=inputFnameLs, **keywords)	#self.connectDB() called within its __init__()
		self.annotation_type_id_list = utils.getListOutOfStr(list_in_str=self.annotation_type_id_list, data_type=int)
		self.annotation_type_id_set = set(self.annotation_type_id_list)
	def __init__(self, inputFnameLs=None, **keywords):
		"""
		"""
		parentClass.__init__(self, inputFnameLs=inputFnameLs, **keywords)
		self.alignmentIDList = utils.getListOutOfStr(list_in_str=self.alignmentIDList, data_type=int)