def check_spelling(checked_word, dist, word_list):
'''
Iterates through word_list and returns the set of all words that are within
edit distance dist of the string checked_word.
'''
# Set constants
ALPHABET = set(list(string.ascii_lowercase))
DIAG_SCORE = 2
OFF_DIAG_SCORE = 1
DASH_SCORE = 0
# contruct scoring matrix over all lower case letters
scoring_matrix = student.build_scoring_matrix(ALPHABET, DIAG_SCORE, OFF_DIAG_SCORE, DASH_SCORE)
# Init list to store words
close_words = []
# Loop over word in word_list
for word in word_list:
# compute alignment matrix
alignment_matrix = student.compute_alignment_matrix(checked_word, word, scoring_matrix, True)
# compute score of global alignments
score, align_x, align_y = student.compute_global_alignment(checked_word, word, scoring_matrix, alignment_matrix)
# calculate edit distance
edit_distance = len(checked_word) + len(word) - score
# Compare edit_distance and dist
if edit_distance <= dist:
# save word
close_words.append(word)
return close_words
def answer_Q7():
alphabet = set(['A', 'C', 'T', 'G'])
diag_score = 2
off_diag_score = 1
dash_score = 0
seq_x = 'AA'
seq_y = 'TAAT'
scoring_matrix = student.build_scoring_matrix(alphabet, diag_score, off_diag_score, dash_score)
alignment_matrix = student.compute_alignment_matrix(seq_x, seq_y, scoring_matrix, True)
score, align_x, align_y = student.compute_global_alignment(seq_x, seq_y, scoring_matrix, alignment_matrix)
edit_distance = len(seq_x) + len(seq_y) - score
return (diag_score, off_diag_score, dash_score)
"""
Algorithmic Thinking - Module 4 Project
Mark Hess
Dynamic Programming and Sequence Alignment
Computing Alginments of sequences
Test File
"""
import Project_4
TEST1 = True
TEST2 = True
TEST3 = False
TEST4 = False
if TEST1:
print (Project_4.build_scoring_matrix(set(['A', 'C', 'T', 'G']), 6, 2, -4))
#expected {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2}, 'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2},
#'-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4}, 'T': {'A': 2, 'C': 2, '-': -4, 'T': 6, 'G': 2},
#'G': {'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6}}
if TEST2:
print (Project_4.compute_alignment_matrix('', '', {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2},
'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2}, '-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4},
'T': {'A': 2, 'C': 2, '-': -4, 'T': 6, 'G': 2}, 'G': {'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6}}, True))
#expected [[0]] but received []
print (Project_4.compute_alignment_matrix('A', 'A', {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2},
'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2}, '-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4},
'T': {'A': 2, 'C': 2, '-': -4, 'T': 6, 'G': 2}, 'G': {'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6}}, True))
#expected [[0, -4], [-4, 6]]
print (Project_4.compute_alignment_matrix('ATG', 'ACG', {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2},
'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2}, '-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4},
Algorithmic Thinking - Module 4 Project
Mark Hess
Dynamic Programming and Sequence Alignment
Computing Alginments of sequences
Test File
"""
import Project_4
TEST1 = False
TEST2 = False
TEST3 = True
TEST4 = True
if TEST1:
print Project_4.build_scoring_matrix(set(['A', 'C', 'T', 'G']), 6, 2, -4)
#expected {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2}, 'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2},
#'-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4}, 'T': {'A': 2, 'C': 2, '-': -4, 'T': 6, 'G': 2},
#'G': {'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6}}
if TEST2:
print Project_4.compute_alignment_matrix('', '', {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2},
'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2}, '-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4},
'T': {'A': 2, 'C': 2, '-': -4, 'T': 6, 'G': 2}, 'G': {'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6}}, True)
#expected [[0]] but received []
print Project_4.compute_alignment_matrix('A', 'A', {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2},
'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2}, '-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4},
'T': {'A': 2, 'C': 2, '-': -4, 'T': 6, 'G': 2}, 'G': {'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6}}, True)
#expected [[0, -4], [-4, 6]]
print Project_4.compute_alignment_matrix('ATG', 'ACG', {'A': {'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2},
'C': {'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2}, '-': {'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4},
