Skip to content

Commit

Permalink
#51 passed sample
Browse files Browse the repository at this point in the history
  • Loading branch information
@weka511
weka511 committed Nov 14, 2020
1 parent 88719c1 commit 45a3392
Showing 1 changed file with 156 additions and 86 deletions.
242 changes: 156 additions & 86 deletions lrep.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,95 +20,145 @@
import time
from helpers import read_strings

class Node:
seq = 0
def __init__(self):
self.Edges = {}
self.Label = None
self.seq = Node.seq
Node.seq += 1
#class Node:
#seq = 0
#def __init__(self):
#self.Edges = {}
#self.Label = None
#self.seq = Node.seq
#Node.seq += 1

def isLeaf(self):
return len(self.Edges)==0
#def isLeaf(self):
#return len(self.Edges)==0

def get_symbols(self):
return list(self.Edges.keys())
#def get_symbols(self):
#return list(self.Edges.keys())

def bfs(self,
prefix = '',
predecessor = None,
visitLeaf = lambda prefix,node:None,
visitInternal = lambda prefix,symbol,node,predecessor:None):
if self.isLeaf():
visitLeaf(prefix,self)
else:
for symbol,edge in self.Edges.items():
visitInternal(prefix,symbol,self,predecessor)
edge.EndingNode.bfs(prefix = prefix + '-',
predecessor = self,
visitLeaf = visitLeaf,
visitInternal = visitInternal)
#def bfs(self,
#prefix = '',
#predecessor = None,
#visitLeaf = lambda prefix,node:None,
#visitInternal = lambda prefix,symbol,node,predecessor:None):
#if self.isLeaf():
#visitLeaf(prefix,self)
#else:
#for symbol,edge in self.Edges.items():
#visitInternal(prefix,symbol,self,predecessor)
#edge.EndingNode.bfs(prefix = prefix + '-',
#predecessor = self,
#visitLeaf = visitLeaf,
#visitInternal = visitInternal)

class Edge:
def __init__(self,EndingNode,Position):
self.EndingNode = EndingNode
self.Position = Position
#class Edge:
#def __init__(self,EndingNode,Position):
#self.EndingNode = EndingNode
#self.Position = Position

def create_suffix_trie(Text):
Trie = Node()
#def create_suffix_trie(Text):
#Trie = Node()

for i in range(len(Text)):
currentNode = Trie
for j in range(i,len(Text)):
currentSymbol = Text[j]
if currentSymbol in currentNode.Edges:
currentNode = currentNode.Edges[currentSymbol].EndingNode
else:
newNode = Node()
newEdge = Edge(newNode,j)
currentNode.Edges[currentSymbol] = newEdge
currentNode = newNode
if currentNode.isLeaf():
currentNode.Label = i
#for i in range(len(Text)):
#currentNode = Trie
#for j in range(i,len(Text)):
#currentSymbol = Text[j]
#if currentSymbol in currentNode.Edges:
#currentNode = currentNode.Edges[currentSymbol].EndingNode
#else:
#newNode = Node()
#newEdge = Edge(newNode,j)
#currentNode.Edges[currentSymbol] = newEdge
#currentNode = newNode
#if currentNode.isLeaf():
#currentNode.Label = i

return Trie
#return Trie

def create_branches(Trie):
def visitInternal(prefix,symbol,node,predecessor,Branches):
if len(node.Edges.items())==1:
if len(predecessor.Edges)>1:
#print (f'<<{predecessor.get_symbols()}')
if len(Branches[-1])>0:
Branches.append([])
Predecessors.append(predecessor)
#Branches[-1].append(predecessor)
Branches[-1].append(node)
#b = ''.join(s for n in Branches[-1] for s in n.get_symbols())
#print (f'{node.seq} {node.get_symbols()} {b}')
else:
if len(Branches[-1])>0:
Branches.append([])
#def create_branches(Trie):

#def visitInternal(prefix,symbol,node,predecessor,Branches):
#if len(node.Edges.items())==1:
#if len(predecessor.Edges)>1:
#if len(Branches[-1])>0:
#Branches.append([])
#Predecessors.append((predecessor,symbol))
#Branches[-1].append(node)

#else:
#if len(Branches[-1])>0:
#Branches.append([])

def visitLeaf(prefix,node,Branches):
if len(Branches[-1])>0:
Branches.append([])
#def visitLeaf(prefix,node,Branches):
#if len(Branches[-1])>0:
#Branches.append([])

Branches = [[]]
Predecessors = []
Trie.bfs(visitLeaf = lambda prefix,node:visitLeaf (prefix,node,Branches),
visitInternal = lambda prefix,symbol,node,predecessor: visitInternal(prefix,symbol,node,predecessor,Branches))
#print( len(Predecessors),len(Branches))
#for b in Branches:
#print (len(b))
if len(Branches[-1])==0:
Branches.pop()
assert len(Predecessors)==len(Branches)
return Branches
#Branches = [[]]
#Predecessors = []
#Trie.bfs(visitLeaf = lambda prefix,node:visitLeaf (prefix,node,Branches),
#visitInternal = lambda prefix,symbol,node,predecessor: visitInternal(prefix,symbol,node,predecessor,Branches))

#if len(Branches[-1])==0:
#Branches.pop()
#assert len(Predecessors)==len(Branches)
#return Branches,Predecessors

def create_suffix_tree(Trie):
pass
#def create_suffix_tree(Trie):
#pass

class Node:
def __init__(self,seq):
self.seq = seq
self.edges = []
def bfs(self,
Nodes,
text,
prefix = '',
visitLeaf = lambda prefix:None,
visitInternal = lambda prefix,symbol:None):
if len(self.edges)==0:
visitLeaf(prefix)
else:
for next_pos,s,l in self.edges:
visitInternal(prefix,text[s:s+l])
Nodes[next_pos].bfs(Nodes,
text,
prefix = prefix + '-',
visitLeaf = visitLeaf,
visitInternal = visitInternal)

def lrep(text,k,edges):
entries = sorted([[int(e.replace('node','')) for e in edge.split()] for edge in edges],key=lambda x:-x[-1])
for i in range(len(entries)):
_,_,pos_i,length_i = entries[i]
if pos_i+length_i>len(text):
length_i-=1
for j in range(i,len(entries)):
_,_,pos_j,length_j = entries[j]
if pos_j==pos_i: continue
if pos_j+length_j>len(text):
length_j-=1
if text[pos_i-1:pos_i-1+length_i]==text[pos_j-1:pos_j-1+length_j]:
while pos_i>1 and pos_j>1 and text[pos_i-2]==text[pos_j-2]:
pos_i -= 1
pos_j -= 1
length_i += 1
return text[pos_i-1:pos_i-1+length_i]


#def create_suffix_tree():
#Nodes = []
#for edge in edges:
#entry = [int(e.replace('node','')) for e in edge.split()]
#while len(Nodes)<max(entry[0],entry[1]):
#Nodes.append(None)
#if Nodes[entry[0]-1] ==None:
#Nodes[entry[0]-1] = Node(entry[0]-1)
#if Nodes[entry[1]-1] ==None:
#Nodes[entry[1]-1] = Node(entry[1]-1)
#Nodes[entry[0]-1].edges.append([entry[1]-1,entry[2]-1,entry[3]])
#return Nodes
#Nodes = create_suffix_tree()
#Nodes[0].bfs(Nodes,s,
#visitInternal = lambda prefix,symbol:print (f'{prefix}{symbol}'))
x=0

if __name__=='__main__':
start = time.time()
Expand All @@ -117,15 +167,35 @@ def create_suffix_tree(Trie):
parser.add_argument('--rosalind', default=False, action='store_true', help='process Rosalind dataset')
args = parser.parse_args()
if args.sample:
Trie = create_suffix_trie('GTCCGAAGCTCCGG$')
Trie.bfs(visitLeaf = lambda prefix,node:print (f'{prefix}{node.Label}'),
visitInternal = lambda prefix,symbol,node,predecessor:print (f'{prefix}{symbol}'))
print ('==========')
for Branch in create_branches(Trie):
symbols = [s for node in Branch for s in node.Edges.keys()]
if len(symbols)>0:
print ('-'.join(symbols))
x=0
print (lrep('CATACATAC$',
2,
['node1 node2 1 1',
'node1 node7 2 1',
'node1 node14 3 3',
'node1 node17 10 1',
'node2 node3 2 4',
'node2 node6 10 1',
'node3 node4 6 5',
'node3 node5 10 1',
'node7 node8 3 3',
'node7 node11 5 1',
'node8 node9 6 5',
'node8 node10 10 1',
'node11 node12 6 5',
'node11 node13 10 1',
'node14 node15 6 5',
'node14 node16 10 1']))
#Trie = create_suffix_trie('GTCCGAAGCTCCGG$')
#Trie.bfs(visitLeaf = lambda prefix,node:print (f'{prefix}{node.Label}'),
#visitInternal = lambda prefix,symbol,node,predecessor:print (f'{prefix}{symbol}'))
#print ('==========')
#Branches,Predecessors = create_branches(Trie)
#for Branch,pre in zip(Branches,Predecessors):
#_,symbol = pre
#symbols = [s for node in Branch for s in node.Edges.keys()]
#if len(symbols)>0:
#print (f'{symbol}-{"".join(symbols)}')
#x=0
#Tree = create_suffix_tree(Trie)


Expand Down

0 comments on commit 45a3392

Please sign in to comment.