def main():
d = build_dict()
############################
# TODO: Build a priority queue based on d
priority_queue = PriorityQueue()
for ch, count in d.items():
tree = Tree(None, ch, None)
priority_queue.enqueue((tree, count))
#priority_queue.traversal()
############################
tree = encoding(priority_queue)
print(decoding(tree, '1010101101010100010100110100000101010101100111'))
def encoding(pq):
"""
:param pq: PriorityQueue, containing all the ch we need to encode
:return: Tree, a binary tree that has all the ch encoded
"""
while True:
left = pq.dequeue()
right = pq.dequeue()
new_value = left.value[1] + right.value[1]
tree = Tree(left.value[0], new_value, right.value[0])
if pq.length() == 0:
return tree
else:
pq.enqueue((tree, new_value))
(gt_E, gt_D, D, gt_T) = tg.generate()
gensNames = list(str(i) for i in range(M))
print(gensNames)
C_num = D.shape[1]
G_num = D.shape[0]
### Run
dl = list(d for d in D)
root = [n for n, d in gt_T.in_degree() if d == 0][0]
print('ROOT:', root)
logfile.write('ROOT:{}\n'.format(root))
T = Tree(gensNames,
D,
data_list=dl,
root=str(root),
alpha=alpha,
beta=beta,
logfile=logfile)
T.set_ground_truth(gt_D, gt_E, gt_T=gt_T)
T.randomize()
for i in range(step_num):
if T.next():
break
# T.plot_all_results()
T.save_mats(prefix_dir)
logfile.close()
break
# except:
edges = [('DNM3', 'ITGAD'), ('ITGAD', 'BTLA'), ('BTLA', 'PAMK3'),
('PAMK3', 'FCHSD2'), ('FCHSD2', 'LSG1'), ('LSG1', 'DCAF8L1'),
('DCAF8L1', 'PIK3CA'), ('PIK3CA', 'CASP3'), ('CASP3', 'TRIM58'),
('TRIM58', 'TCP11'), ('TCP11', 'MARCH11'), ('MARCH11', 'DUSP12'),
('DUSP12', 'PPP2RE'), ('PPP2RE', 'ROPN1B'), ('ROPN1B', 'PITRM1'),
('PITRM1', 'FBN2'), ('FBN2', 'PRDM9'), ('FBN2', 'GPR64'),
('PRDM9', 'CABP2'), ('PRDM9', 'ZEHX4'), ('PRDM9', 'H1ENT'),
('PRDM9', 'WDR16'), ('CABP2', 'TRIB2'), ('ZEHX4', 'DKEZ'),
('WDR16', 'GLCE'), ('GLCE', 'CALD1'), ('CABP2', 'C15orf23'),
('CABP2', 'CNDP1'), ('CNDP1', 'CXXX1'), ('CNDP1', 'c1orf223'),
('CXXX1', 'FUBP3'), ('c1orf223', 'TECTA'), ('GPR64', 'MUTHY'),
('MUTHY', 'SEC11A'), ('SEC11A', 'KIAA1539'), ('SEC11A', 'RABGAP1L'),
('RABGAP1L', 'ZNE318'), ('KIAA1539', 'FGFR2'), ('FGFR2', 'PLXNA2')]
dl = list(d for d in D)
SNT = Tree(gensNames, D=D, data_list=dl, name='Paper Tree')
SNT.set_edges(edges, remove_edges=True)
_.print_bold('SCITE Navis\'s Tree Error:', SNT.get_best_error())
SNT.plot_best_T('paper_tree')
### Run
dl = list(d for d in D)
T = Tree(gensNames, D=D, data_list=dl)
# edges = [('PIK3CA', 'c1orf223'),('PIK3CA', 'TCP11'),('DNM3', 'ITGAD'),('TRIM58', 'DUSP12'),('DCAF8L1', 'FCHSD2'),('DCAF8L1', 'GLCE'),('FBN2', 'PPP2RE'),('FCHSD2', 'LSG1'),('CASP3', 'PITRM1'),('CASP3', 'RABGAP1L'),('ITGAD', 'DCAF8L1'),('PPP2RE', 'ROPN1B'),('LSG1', 'PIK3CA'),('ROPN1B', 'MARCH11'),('BTLA', 'FBN2'),('DUSP12', 'BTLA'),('MARCH11', 'CASP3'),('MARCH11', 'CALD1'),('TCP11', 'TRIM58'),('TCP11', 'CNDP1'),('PITRM1', 'PRDM9'),('PITRM1', 'ZEHX4'),('PITRM1', 'MUTHY'),('PITRM1', 'CXXX1'),('PRDM9', 'CABP2'),('PRDM9', 'PAMK3'),('MUTHY', 'FGFR2'),('GPR64', 'TRIB2'),('SEC11A', 'C15orf23'),('SEC11A', 'PLXNA2'),('C15orf23', 'H1ENT'),('DKEZ', 'FUBP3'),('FUBP3', 'WDR16'),('WDR16', 'GPR64'),('RABGAP1L', 'TECTA'),('RABGAP1L', 'ZNE318'),('RABGAP1L', 'KIAA1539'),('RABGAP1L', 'SEC11A'),('GLCE', 'DKEZ')]
# T.set_edges(edges, remove_edges=True)
T.randomize()
T.plot_best_T('sn_initial_tree')
# T.set_edges(edges, remove_edges=True)
for i in range(10):