def __init__(self, **keywords): """ 2012.5.05 """ inputFnameLs = [] AbstractVervetMapper.__init__(self, inputFnameLs, **keywords)
def __init__(self, inputFnameLs=None, **keywords):
"""
"""
AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
listArgumentName_data_type_ls = [("site_id_ls", int), ('country_id_ls', int), ('tax_id_ls', int)]
listArgumentName2hasContent = ProcessOptions.processListArguments(listArgumentName_data_type_ls,\
emptyContent=[], class_to_have_attr=self)
def __init__(self, inputFnameLs=None, **keywords): """ pop_gen_simulation_type_id=None, replicate_index=None, \ no_of_populations=None,\ no_of_chromosomes=None, chromosome_length=None, sample_size=None, \ no_of_polymorphic_loci=None, """ AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs=None, **keywords):
"""
"""
AbstractVervetMapper.__init__(self,
inputFnameLs=inputFnameLs,
**keywords)
listArgumentName_data_type_ls = [("site_id_ls", int),
('country_id_ls', int),
('tax_id_ls', int)]
ProcessOptions.processListArguments(listArgumentName_data_type_ls,\
emptyContent=[], class_to_have_attr=self)
def __init__(self, inputFnameLs=None, **keywords):
"""
"""
AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
if self.monkey1ID and self.monkey2ID:
self.monkeyPairDesignated = [self.monkey1ID, self.monkey2ID]
self.monkeyPairDesignated.sort()
self.monkeyPairDesignated = tuple(self.monkeyPairDesignated)
else:
self.monkeyPairDesignated = None
yh_matplotlib.setFontAndLabelSize(self.defaultFontLabelSize)
yh_matplotlib.setDefaultFigureSize((self.defaultFigureWidth, self.defaultFigureHeight))
def __init__(self, inputFnameLs=None, **keywords): """ """ AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords) #self.connectDB() called within its __init__()
def __init__(self, inputFnameLs=None, **keywords): """ """ AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def __init__(self, inputFnameLs=None, **keywords):
"""
"""
AbstractVervetMapper.__init__(self,
inputFnameLs=inputFnameLs,
**keywords)
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): """ """ AbstractVervetMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords) self.inputFname= os.path.realpath(self.inputFname)
def __init__(self, **keywords): """ """ AbstractVervetMapper.__init__(self, inputFnameLs=None, **keywords) #connectDB(), and setup srcFilenameLs and dstFilenameLs
def __init__(self, inputFnameLs, **keywords):
"""
"""
AbstractVervetMapper.__init__(self, inputFnameLs, **keywords)
self.sequence2DBentry = {} #2012.5.2 a cache to store the relevant db entries for sequence