def __init__(self): SampleStat.__init__(self) self.type2gene2clones = {} self.type2gene2reads = {} types = ['v', 'd', 'j', 'vj', 'dj'] for type in types: self.type2gene2clones[type] = {} self.type2gene2reads[type] = {}
def __init__(self, v2freq, j2freq, len2freq, color, marker, name): SampleStat.__init__(self) self.type2gene2clones = {} self.type2gene2clones['v'] = v2freq self.type2gene2clones['j'] = j2freq self.len2clones = len2freq self.color = color self.marker = marker self.name = name
def __init__(self, freqs=[]): SampleStat.__init__(self) if freqs: self.freqs = freqs else: #self.freqs = [0, 0.001, 0.01, 0.1, 1] self.freqs = [0, 0.00001, 0.0001, 0.001, 0.01] self.numclones = [0.0] * len(self.freqs) self.counts = [0.0] * len(self.freqs) self.topfreqs = [] # frequencies of the top clones self.numclones_cumul = self.numclones # cumulative self.counts_cumul = self.counts # cumulative self.topfreqs_cumul = [] # cumulative freqs of top clones
def __init__(self): SampleStat.__init__(self) #self.numclone = None # R vegan: diversity self.simpson = None self.invsimpson = None self.shannon = None self.fisher_alpha = None # Standard deviation self.numclone_std = None self.simpson_std = None self.invsimpson_std = None self.shannon_std = None self.fisher_alpha_std = None
def __init__(self): SampleStat.__init__(self) self.len2clones = {} self.len2reads = {} self.median_clones = None # median cdr3 length based on # clones self.median_reads = None # median cdr3 length based on # reads