Exemplo n.º 1
0
 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] = {}
Exemplo n.º 2
0
 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
Exemplo n.º 3
0
 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
Exemplo n.º 4
0
    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
Exemplo n.º 5
0
 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