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('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('humanmethylation'))