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trie.py
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trie.py
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'''http://rosalind.info/problems/trie/'''
class Trie(object):
def __init__(self, seqCollection = None):
'''Initialize a Trie, can be empty.'''
self.allSeqs = seqCollection
self.trie = {(1, 'Root'): set()}
self.done = False
self.autoIncrement = 1
def buildTrie(self, seqCollection = None):
'''Build the trie with given list of sequences. Can be run multiple times.'''
if self.allSeqs == None:
self.allSeqs = seqCollection
else:
if seqCollection != None:
self.allSeqs.extend(seqCollection)
assert self.allSeqs != None, 'Please give a list of strings'
for seq in self.allSeqs:
self._mergeOneSeq(seq)
self.done = True
def _mergeOneSeq(self, seq):
currentNode = (1, 'Root')
for n in seq:
foundMatch = False
nodeID = None
for follower in self.trie[currentNode]:
if follower[1] == n:
foundMatch = True
nodeID = follower[0]
currentNode = follower
break
if not foundMatch:
self.autoIncrement += 1
self.trie[currentNode].add((self.autoIncrement, n))
self.trie[(self.autoIncrement, n)] = set()
currentNode = (self.autoIncrement, n)
def rosalindOutput(self):
assert self.done, 'Please run all calculation first.'
for node, followers in self.trie.items():
for f in followers:
print(node[0], f[0], f[1])
def main():
seqText = open('rosalind_trie.txt', 'r').read()
seqCollection = seqText.splitlines()
trie = Trie()
trie.buildTrie(seqCollection)
'''
# Test for run Trie.buildTrie() multiple times
a = ['QQQB', 'QQQA']
trie.buildTrie(a)
'''
trie.rosalindOutput()
if __name__ == '__main__':
main()