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algorithm_needleman_wunsch.py
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algorithm_needleman_wunsch.py
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import sys, os
from os import listdir
from os.path import isfile, join
import numpy as np
class needleman_wunsch(object):
def __init__(self, user_input, requested_database_filenames):
self.user_input = [
letter
for letters in [line for line in user_input[user_input.find("\n")+1:] if len(line) > 0]
for letter in letters if letter != '\n'
]
self.substitution_symbols = []
self.substitution_values = []
self.overall_results = []
self.gap_value = -1
self.init_shared_parameters()
if len(requested_database_filenames) == 1 and os.path.isdir(requested_database_filenames[0]):
requested_database_filenames = [requested_database_filenames[0] + f for f in listdir(requested_database_filenames[0]) if isfile(join(requested_database_filenames[0], f))]
for filename in requested_database_filenames:
self.database_sequence = []
self.scoring_matrix = []
self.read_from_files(filename)
self.finalresults = []
self.needleman_wunsch()
def return_overall_results(self):
return self.overall_results
def read_from_files(self, filename):
openfile = open(filename, 'r', encoding="utf-8")
readfile = openfile.read().split('\n')
self.database_sequence = [
letter
for letters in [line for line in readfile[1:] if len(line) > 0]
for letter in letters
]
openfile.close()
def init_shared_parameters(self):
openfile = open(
'hyperparameters/substitution_matrix_example_needleman_wunsch.txt',
'r', encoding="utf-8")
readfile = openfile.read().split('\n')
self.substitution_symbols
self.substitution_symbols = [
symbol for symbol in readfile[0] if symbol != ' '
]
self.substitution_values
self.substitution_values = [
list(map(int, number)) for number in
[line.split(' ') for line in readfile[1:] if len(line) > 0]
]
openfile.close()
def maxtuple(self, *args):
maxval = [-1000, -1, -1]
for arg_index in range(len(args)):
maxval = (args[arg_index], maxval)[args[arg_index][0] < maxval[0]]
maxvaltuple = [maxval]
for arg_index in range(len(args)):
if args[arg_index][0] == maxval[0] and (
args[arg_index][1] != maxval[1] or
args[arg_index][2] != maxval[2]):
maxvaltuple.append(args[arg_index])
if len(maxvaltuple) > 1:
return maxvaltuple
else:
return maxval
def get_substitution_value(self, a, b):
a_index = self.substitution_symbols.index(a)
b_index = self.substitution_symbols.index(b)
return self.substitution_values[a_index][b_index]
def backtracking(self, max_score, result=[]):
while max_score[0] >= 0 and max_score[1] > 0 and max_score[2] > 0:
substitution_value = self.get_substitution_value(
self.database_sequence[max_score[1] - 1],
self.user_input[max_score[2] - 1])
max_score_temp = self.maxtuple (\
[self.scoring_matrix[max_score[1]-1][max_score[2]-1]+substitution_value , max_score[1]-1 , max_score[2]-1],\
[self.scoring_matrix[max_score[1]][max_score[2]-1]+self.gap_value,max_score[1],max_score[2]-1],\
[self.scoring_matrix[max_score[1]-1][max_score[2]]+self.gap_value,max_score[1]-1,max_score[2]])
if type(max(max_score_temp)) == list:
for tuple_index in range(len(max_score_temp)):
if max_score[2] != max_score_temp[tuple_index][2] and max_score[1] != max_score_temp[tuple_index][1]:
tempresult = [[
self.database_sequence[max_score[1] - 1],
self.user_input[max_score[2] - 1]
]] + result
elif max_score[2] != max_score_temp[tuple_index][2] and max_score[1] == max_score_temp[tuple_index][1]:
tempresult = [['-', self.user_input[max_score[2] - 1]]
] + result
elif max_score[2] == max_score_temp[tuple_index][2] and max_score[1] != max_score_temp[tuple_index][1]:
tempresult = [[
self.database_sequence[max_score[1] - 1], '-'
]] + result
self.backtracking(
[
self.scoring_matrix[max_score_temp[tuple_index][1]]
[max_score_temp[tuple_index][2]],
max_score_temp[tuple_index][1],
max_score_temp[tuple_index][2]
],
result=tempresult)
return
else:
if max_score[2] != max_score_temp[2] and max_score[1] != max_score_temp[1]:
result = [[
self.database_sequence[max_score[1] - 1],
self.user_input[max_score[2] - 1]
]] + result
elif max_score[2] != max_score_temp[2] and max_score[1] == max_score_temp[1]:
result = [['-', self.user_input[max_score[2] - 1]]] + result
elif max_score[2] == max_score_temp[2] and max_score[1] != max_score_temp[1]:
result = [[self.database_sequence[max_score[1] - 1], '-']
] + result
max_score = [
self.scoring_matrix[max_score_temp[1]][max_score_temp[2]],
max_score_temp[1], max_score_temp[2]
]
self.finalresults.append(result)
def needleman_wunsch(self):
self.scoring_matrix = [[
-1 * x + (-1 * y) for x in range(len(self.user_input) + 1)
] for y in range(len(self.database_sequence) + 1)]
for index_i, element_i in enumerate(self.database_sequence):
for index_j, element_j in enumerate(self.user_input):
substitution_value = self.get_substitution_value(
element_i, element_j)
self.scoring_matrix[index_i + 1][index_j + 1] = max(
self.scoring_matrix[index_i][index_j] + substitution_value,
self.scoring_matrix[index_i][index_j + 1] + self.gap_value,
self.scoring_matrix[index_i + 1][index_j] + self.gap_value)
self.last_score = [
self.scoring_matrix[len(self.database_sequence)][len(
self.user_input)],
len(self.database_sequence),
len(self.user_input)
]
if type(max(self.last_score)) == list:
self.last_score = self.last_score[0]
self.backtracking(self.last_score)
self.overall_results.append(self.finalresults)
if __name__ == '__main__':
nw = needleman_wunsch('GCATGCU', [
'database/database_sequence_example_smith_waterman.fa',
'database/database_sequence_example_needleman_wunsch.fa'
])
print(nw.return_overall_results())