def transform(self, s):
""" Burrows-Wheeler transform with SuffixTree """
assert self.EOS not in s, "Input string cannot contain null character ('%s')" % self.EOS
# add end of text marker
s += self.EOS
st = SuffixTree()
# construct a suffix tree O(n * log n)
# can also be done in O(n) time
st.add(s)
# walk inorder to find sorted suffixes
# only get the length of each suffix
lens = self._walk(st.root)
# as the last column letter will be left of the suffix
# this means it's len(suffix) + 1
# from the end of the input string s
r = [0] * len(lens)
for i in xrange(len(lens)):
l = lens[i]
if l == len(lens):
r[i] = self.EOS
else:
r[i] = s[-l - 1]
return ''.join(r)
def transform(self, s):
""" Burrows-Wheeler transform with SuffixTree """
assert self.EOS not in s, "Input string cannot contain null character ('%s')" % self.EOS
# add end of text marker
s += self.EOS
st = SuffixTree()
# construct a suffix tree O(n * log n)
# can also be done in O(n) time
st.add(s)
# walk inorder to find sorted suffixes
# only get the length of each suffix
lens = self._walk(st.root)
# as the last column letter will be left of the suffix
# this means it's len(suffix) + 1
# from the end of the input string s
r = [0]*len(lens)
for i in xrange(len(lens)):
l = lens[i]
if l == len(lens):
r[i] = self.EOS
else:
r[i] = s[-l-1]
return ''.join(r)
def __init__(self, dna):
self.dna = dna
self.suffix_tree = SuffixTree(len(dna))
self.suffix_array = []
self.first_col = []
self.bwt = []
self.ltof = []
self.init_self()
def suffix_search_lcs(a, b):
# left and right bounds, max sizes
len_a, len_b = len(a) + 1, len(b) + 1
short = min(len(a), len(b))
tree = SuffixTree(False, [a])
# returns if there is a common substring of length m between a, b
def found_common(m):
return any(tree.findStringIdx(b[i-m:i]) for i in range(m, len_b))
# exponentially increase l and r
l, r = 0, 1
while r < len_a and found_common(r):
l, r = r + 1, r * 2
r = min(r, short)
# right-most binary search on if substring length is possible
while l <= r:
m = (l + r) // 2
if found_common(m):
l = m + 1
else:
r = m - 1
return r
class Notebook(object):
"""
Notebook object that represents a single text document that is loaded
into memory to allow the program to query and report information about
its contents. The core logic of the program should be found within this
class.
"""
def __init__(self, file_path):
self.file_path = file_path
self.suffix_tree = SuffixTree()
self._parse_file(self.file_path)
def reload(self, file_path=None):
if file_path:
self.file_path = file_path
self.suffix_tree.root = Node() # Restart the suffix tree
self._parse_file(self.file_path)
def _parse_file(self, file_path):
with open(file_path,'r') as notebook:
# build the contents found in the file
for i, line in enumerate(notebook.readlines()):
word = '' # word buffer
start = -1
for j, char in enumerate(line):
if char in WHITE_KEYS or char in SPECIAL_CHARS:
self._add_suffixes(word, start, i)
word = ''
start = -1
else:
if start==-1:
start = j
word += char
# Adds a word and all of its suffixes
def _add_suffixes(self, word, position, line_no, whole_word=True):
if len(word) == 0:
return
self.suffix_tree.add_word(word.lower(), ((position, line_no), whole_word))
def suffix_search_lcs(a, b):
# left and right bounds, max sizes
len_a, len_b = len(a) + 1, len(b) + 1
short = min(len(a), len(b))
tree = SuffixTree(True, [a])
print('Completed suffix tree')
# returns if there is a common substring of length m between a, b
def found_common(m):
return any(tree.findStringIdx(b[i - m:i]) for i in range(m, len_b))
# exponentially increase l and r
l, r = 0, 1
print(l, r)
while r < len_a and found_common(r):
l, r = r + 1, r * 2
print(l, r)
r = min(r, short)
print(l, r)
# right-most binary search on if substring length is possible
while l <= r:
m = (l + r) // 2
print(m)
if found_common(m):
l = m + 1
else:
r = m - 1
print('Longest Common Substrings:')
print('\n'.join(
set(b[i - r:i] for i in range(r, len_b)
if tree.findStringIdx(b[i - r:i]))))
return r
@dataclass
class Point:
lat: float
lon: float
def __hash__(self) -> int:
return hash((self.lat, self.lon))
def __eq__(self, o: object) -> bool:
return self.__hash__() == o.__hash__()
def __str__(self) -> str:
return f'{self.lat},{self.lon}'
s = SuffixTree()
s.generate(
(
Point(1,1),
Point(1,0),
Point(0,1),
Point(1,1),
Point(1,0),
Point(0,0),
)
)
# s.generate('MISSISSIPPI$')
# annotate graph for vizualization
for i in range(1, s.order()):
parent = s.parent_id(i)
'''
Created on Oct 23, 2018
@author: ckennington
'''
from stlm import STLM
from suffixtree import SuffixTree
from sequence import Sequence
trie = SuffixTree()
text = 'c a c a o'.split()
for w in text:
print('adding', w)
trie.add(w)
print('\n')
trie.print_tree()
print('\n')
trie.update_all_counts()
stlm = STLM(trie)
tests = [
'c a'.split(), 'c a o'.split(), 'a o'.split(), 'o'.split(), 'c'.split()
]
for test in tests:
seq = Sequence()
class Mapper:
def __init__(self, dna):
self.dna = dna
self.suffix_tree = SuffixTree(len(dna))
self.suffix_array = []
self.first_col = []
self.bwt = []
self.ltof = []
self.init_self()
def init_self(self):
"""initializes lists needed for mapping"""
for c in self.dna:
self.suffix_tree.add_char(c)
root = self.suffix_tree.nodes[self.suffix_tree.root]
self.traverse_tree(root, root.start)
self.first_col = create_subscripts(
[self.dna[x] for x in self.suffix_array])
self.bwt = create_subscripts([
self.dna[x - 1] if x > 0 else self.dna[-1]
for x in self.suffix_array
])
self.ltof = [self.first_col.index(x) for x in self.bwt]
def traverse_tree(self, node, char_depth):
"""traverse the tree recursively to generate suffix array"""
if not node.edges:
self.suffix_array.append(node.start - char_depth - 1)
return
chars = ['$', 'A', 'C', 'G', 'T']
for char in chars:
try:
next_node = self.suffix_tree.nodes[node.edges[char]]
new_depth = char_depth + (node.end - node.start)
self.traverse_tree(next_node, new_depth)
except KeyError:
pass
def get_position_range(self, char, list_type, start, end):
"""returns range of positions for a char in specified type of list"""
positions = []
for index in xrange(start, end + 1):
if list_type[index].startswith(char):
positions.append(index)
break
for index in xrange(end, start, -1):
if list_type[index].startswith(char):
positions.append(index)
break
return positions
def map(self, pattern):
"""find a given pattern in the genome"""
found_positions = []
rev_pattern = pattern[::-1]
current_positions = self.get_position_range(rev_pattern[0],
self.first_col, 0,
len(self.first_col) - 1)
for i in xrange(1, len(rev_pattern)):
try:
bwt_positions = self.get_position_range(
rev_pattern[i], self.bwt, current_positions[0],
current_positions[-1])
ltof_positions = range(self.ltof[bwt_positions[0]],
self.ltof[bwt_positions[-1]] + 1)
current_positions = ltof_positions
except IndexError:
# may not be able to find, simply return so don't have to go through entire pattern
return found_positions
# after last char, push every position in SA to found_positions
for i in current_positions:
found_positions.append(self.suffix_array[i])
return found_positions
def __init__(self, file_path):
self.file_path = file_path
self.suffix_tree = SuffixTree()
self._parse_file(self.file_path)
