def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('nationwidechildrens_org_microsat_i'))
self.tokenFeature2Index = int(self.configuration['token_feature_2_index'])
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('mdanderson_org_mda_rppa_core'))
self.fname2row = {}
self.topRowIndex = 0
self.gene2ab = {}
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('mdanderson_org_mda_rppa_core'))
self.fname2row = {}
self.topRowIndex = 0
self.gene2ab = {}
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('genome_wide_snp_6'))
self.translate = dict([[cn for cn in x.split(':')] for x in self.configuration['chr_translate'].split(',')])
self.stripPrefixes = self.configuration['chr_strip_prefixes'].split(',')
self.chr2data = {}
self.chr2maxcoord = {}
for index in range(1, 25):
chrom = self._unifychr(str(index))
self.chr2data[chrom] = AutoVivification()
self.chr2maxcoord[chrom] = 0
resegment.NA_VALUE = int(self.configuration['na_value'])
resegment.NEAR_ZERO = float(self.configuration['near_zero'])
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('clinical'))
## initialize empty dictionary for clinical data
self.allClinDict = {}
self.curFileCount = 0
## get the stings needed for processing tags
self.excludePrefix = self.configuration['excludeprefix'].split(',')
self.excludeSuffix = self.configuration['excludesuffix'].split(',')
self.excludeStrings = self.configuration['excludestrings'].split(',')
self.includeStrings = self.configuration['includestrings'].split(',')
self.removePrefix = [pre.split(':') for pre in self.configuration['removeprefix'].split(',')]
self.sharedBarcodeKey = self.configuration['sharedbarcode']
self.featNamesLoaded = 0
self.featNamesDict = {}
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('clinical'))
## initialize empty dictionary for clinical data
self.allClinDict = {}
self.curFileCount = 0
## get the stings needed for processing tags
self.excludePrefix = self.configuration['excludeprefix'].split(',')
self.excludeSuffix = self.configuration['excludesuffix'].split(',')
self.excludeStrings = self.configuration['excludestrings'].split(',')
self.includeStrings = self.configuration['includestrings'].split(',')
self.removePrefix = [
pre.split(':')
for pre in self.configuration['removeprefix'].split(',')
]
self.sharedBarcodeKey = self.configuration['sharedbarcode']
self.featNamesLoaded = 0
self.featNamesDict = {}
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('unc_edu_agilentg4502a_07'))
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('illumina_rnaseq'))
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('broad_mit_edu_ht_hg-u133a'))
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('h-mirna_8x15k'))
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('unc_edu_agilentg4502a_07'))
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('humanmethylation'))
def __init__(self, config, platformID):
'''
Constructor
'''
technology_type.__init__(self, config, platformID)
self.configuration.update(config.items('illumina_rnaseq'))
