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 connectDB(self): """ 2012.4.29 split out of __init__() so that derived classes could overwrite this function """ AbstractVervetMapper.connectDB(self) db_taxonomy = TaxonomyDB.TaxonomyDB(drivername=self.drivername, db_user=self.db_user, db_passwd=self.db_passwd, \ hostname=self.hostname, dbname=self.dbname, schema="taxonomy", port=self.port) db_taxonomy.setup(create_tables=False) self.db_taxonomy = db_taxonomy
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 connectDB(self): """ 2012.5.14 2012.4.29 split out of __init__() so that derived classes could overwrite this function """ AbstractVervetMapper.connectDB(self) db_genome = GenomeDB.GenomeDatabase(drivername=self.drivername, db_user=self.db_user, db_passwd=self.db_passwd, hostname=self.hostname, dbname=self.dbname, \ schema=self.genome_db_schema, port=self.port) db_genome.setup(create_tables=False) #do the setup() after both db have been instantiated. self.db_genome = db_genome
def connectDB(self):
"""
2012.4.29
split out of __init__() so that derived classes could overwrite this function
"""
AbstractVervetMapper.connectDB(self)
db_taxonomy = TaxonomyDB.TaxonomyDB(drivername=self.drivername,
hostname=self.hostname,
dbname=self.dbname,
schema="taxonomy",
port=self.port,
db_user=self.db_user,
db_passwd=self.db_passwd)
db_taxonomy.setup(create_tables=False)
self.db_taxonomy = db_taxonomy
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