def __init__(self, inputFnameLs=None, **keywords):
"""
"""
self.ad = ProcessOptions.process_function_arguments(keywords, \
self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
if getattr(self, 'outputFname', None) and hasattr(self,'outputFnamePrefix'):
self.outputFnamePrefix = os.path.splitext(self.outputFname)[0]
self.inputFnameLs = inputFnameLs
if self.inputFnameLs is None:
self.inputFnameLs = []
if getattr(self, 'inputFname', None):
self.inputFnameLs.insert(0, self.inputFname)
#2013.08.14 setup self.inputFname if self.inputFnameLs is not None
if self.inputFnameLs and not getattr(self, 'inputFname', None):
self.inputFname = self.inputFnameLs[0]
if getattr(self, 'inputDelimiter', None):
if self.inputDelimiter=='tab':
self.inputDelimiter = '\t'
if self.inputDelimiter=='space':
self.inputDelimiter = ' '
if self.inputDelimiter=='coma':
self.inputDelimiter = ','
self.connectDB()
#2012.8.14 an expression that searches any character in a string
self.p_char = re.compile(r'[a-df-zA-DF-Z\-]$')
def __init__(self, refNameLs, **keywords):
"""
2011-7-11
"""
self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
self.refNameLs = refNameLs
def __init__(self, **keywords):
"""
"""
self.ad = ProcessOptions.process_function_arguments(
keywords,
self.option_default_dict,
error_doc=self.__doc__,
class_to_have_attr=self)
def __init__(self, inputFnameLs, **keywords):
"""
2011-11-4
"""
from palos import ProcessOptions
self.ad = ProcessOptions.process_function_arguments(keywords,
self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
self.inputFnameLs = inputFnameLs
def __init__(self, **keywords):
"""
2008-05-18
"""
from palos import ProcessOptions
self.ad = ProcessOptions.process_function_arguments(
keywords,
self.option_default_dict,
error_doc=self.__doc__,
class_to_have_attr=self)
def __init__(self, **keywords):
"""
2008-12-02
modelled after ConvertYuSNPFormat2Bjarni.py
"""
from palos import ProcessOptions
self.ad = ProcessOptions.process_function_arguments(
keywords,
self.option_default_dict,
error_doc=self.__doc__,
class_to_have_attr=self)
def __init__(self, **keywords):
"""
2011-7-12
"""
self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
self.discoverFuncDict = {
1: self.discoverFromVCF,
2: self.discoverFromBAM,
3: self.discoverFromVCFWithoutFilter
}
def __init__(self, **keywords):
"""
2008-09-17
allow priority=3 or 4
2008-06-02
"""
self.ad = ProcessOptions.process_function_arguments(
keywords,
self.option_default_dict,
error_doc=self.__doc__,
class_to_have_attr=self)
def __init__(self, **keywords):
"""
"""
self.ad = ProcessOptions.process_function_arguments(keywords,
self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
self.inf = None
self._initializeInput(inputFname=self.inputFname)
self._seqTitle2sequence = None
self._seqTitleList = None #2013.07.08
self.outf = None
def __init__(self, **keywords):
"""
2008-07-27
"""
from palos import ProcessOptions
self.ad = ProcessOptions.process_function_arguments(
keywords,
self.option_default_dict,
error_doc=self.__doc__,
class_to_have_attr=self)
self.table_names = self.table_names.split(',')
self.printTriggerDict = {1: self.printPostGresTrigger,\
2: self.printMySQLTrigger}