def __init__(self, pheno_seq, haps, loci):
phenotype.phenotype_count += 1
print 'creating phenotype %d ...' % phenotype.phenotype_count
self.count = 1
self.loci = loci
self.g_size = self.loci[0].g_size
self.haps = haps
self.name = phenotype.create_name(pheno_seq, loci)
self.hap_sets = {} # (hap_seq1, hap_seq2 ... hap_seqg_size) : weight
hap_seq_sets = []
self.generate_hap_seq_sets(pheno_seq, hap_seq_sets)
# - Add any new haplotypes to the master haplotype dictionary.
#
for set in hap_seq_sets:
for hap_seq in set:
if not hap_seq in self.haps.haps:
self.haps[hap_seq] = haplotype(hap_seq, self.loci)
self.hap_sets[tuple(set)] = None
self.ambiguous = len(self.hap_sets) > 1
self.init_weights()
def __init__(self, pheno_seq, haps, loci):
phenotype.phenotype_count += 1
print 'creating phenotype %d ...' % phenotype.phenotype_count
self.count = 1
self.loci = loci
self.g_size = self.loci[0].g_size
self.haps = haps
self.name = phenotype.create_name(pheno_seq, loci)
self.hap_sets = {} # (hap_seq1, hap_seq2 ... hap_seqg_size) : weight
self.hap_set_counts = {
} # (hap_seq1, hap_seq2 ... hap_seqg_size) : dictionary of haplotype counts
hap_seq_sets = [] # keys to hap_sets
self.generate_hap_seq_sets(pheno_seq, hap_seq_sets)
# - Add any new haplotypes to the master haplotype dictionary.
#
for set in hap_seq_sets:
for hap_seq in set:
if not hap_seq in self.haps.haps:
self.haps[hap_seq] = haplotype(hap_seq, self.loci)
self.hap_sets[tuple(set)] = None
self.ambiguous = len(self.hap_sets) > 1
self.init_weights()
for set in self.hap_sets.keys():
self.hap_set_counts[set] = phenotype.copy_counts(set)
def __init__(self, pheno_seq, haps, loci):
self.count = 1
self.hap_pairs = {}
hap_seq_pairs = []
self.generate_hap_seq_pairs(pheno_seq, hap_seq_pairs, loci)
# - Add any new haplotypes to set of haplotypes.
#
for pair in hap_seq_pairs:
first = tuple(pair[0])
if not haps.has_key(first):
haps[first] = haplotype(first, loci)
second = tuple(pair[1])
if not haps.has_key(second):
haps[second] = haplotype(second, loci)
self.hap_pairs[(first, second)] = None
self.ambiguous = len(self.hap_pairs) > 1
self.init_weights()