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.getRealPrefixSuffix(
self.inputFname)[1][1:]
else:
self.inputFileFormat = self.fileFormatDict.get(
self.inputFileFormat)
if not self.outputFileFormat: #0 or None or ''
self.outputFileFormat = utils.getRealPrefixSuffix(
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):
"""
"""
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, **keywords):
"""
"""
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, inputFnameLs=None, **keywords):
"""
"""
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 __init__(self, inputFnameLs=None, **keywords):
"""
self.missingDataNotation will be processed into a set.
"""
#self.connectDB() called within its __init__()
AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
#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 addObjectListAttributeToSet(self,
attributeName=None,
setVariable=None,
data_type=None):
"""
"""
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):
"""
"""
ParentClass.__init__(self, inputFnameLs=inputFnameLs, **keywords)
self.alignmentIDList = utils.getListOutOfStr(
list_in_str=self.alignmentIDList, data_type=int)