def random_alignment(scoring_matrix):
'''
Take two random amino acids, compute the alignment and the consensus with pax
Return the ratio of similarity
To examine the solution of the homework
'''
alphabet = "ACBEDGFIHKMLNQPSRTWVYXZ"
length_human = 422
length_fruitfly = 857
random_human = ''
for _ in range(length_human):
random_human += random.choice(alphabet)
random_fruitfly = ''
for _ in range(length_fruitfly):
random_fruitfly += random.choice(alphabet)
alignment_matrix = compute_alignment_matrix(seq_x=random_human, seq_y=random_fruitfly, scoring_matrix=scoring_matrix, global_flag=False)
score, align_human, align_fruitfly = compute_local_alignment(seq_x=random_human, seq_y=random_fruitfly, scoring_matrix=scoring_matrix, alignment_matrix=alignment_matrix)
global_align_human, ratio_human_random = consensus_alignment(scoring_matrix, align_human)
global_align_fruitfly, ratio_fruitfly_random = consensus_alignment(scoring_matrix, align_fruitfly)
return ratio_human_random, ratio_fruitfly_random
def random_alignment(scoring_matrix):
'''
Take two random amino acids, compute the alignment and the consensus with pax
Return the ratio of similarity
To examine the solution of the homework
'''
alphabet = "ACBEDGFIHKMLNQPSRTWVYXZ"
length_human = 422
length_fruitfly = 857
random_human = ''
for _ in range(length_human):
random_human += random.choice(alphabet)
random_fruitfly = ''
for _ in range(length_fruitfly):
random_fruitfly += random.choice(alphabet)
alignment_matrix = compute_alignment_matrix(seq_x=random_human,
seq_y=random_fruitfly,
scoring_matrix=scoring_matrix,
global_flag=False)
score, align_human, align_fruitfly = compute_local_alignment(
seq_x=random_human,
seq_y=random_fruitfly,
scoring_matrix=scoring_matrix,
alignment_matrix=alignment_matrix)
global_align_human, ratio_human_random = consensus_alignment(
scoring_matrix, align_human)
global_align_fruitfly, ratio_fruitfly_random = consensus_alignment(
scoring_matrix, align_fruitfly)
return ratio_human_random, ratio_fruitfly_random
def protein_alignment(scoring_matrix):
'''
compute the human eyeless protein and fruitfly eyeless portein alignment
'''
human_protein = read_protein('HumanEyelessProtein.txt')
fruitfly_protein = read_protein('FruitflyEyelessprotein.txt')
alignment_matrix = compute_alignment_matrix(seq_x=human_protein, seq_y=fruitfly_protein, scoring_matrix=scoring_matrix, global_flag=False)
score, align_human, align_fruitfly = compute_local_alignment(seq_x=human_protein, seq_y=fruitfly_protein, scoring_matrix=scoring_matrix, alignment_matrix=alignment_matrix)
return score, align_human, align_fruitfly
def protein_alignment(scoring_matrix):
'''
compute the human eyeless protein and fruitfly eyeless portein alignment
'''
human_protein = read_protein('HumanEyelessProtein.txt')
fruitfly_protein = read_protein('FruitflyEyelessprotein.txt')
alignment_matrix = compute_alignment_matrix(seq_x=human_protein,
seq_y=fruitfly_protein,
scoring_matrix=scoring_matrix,
global_flag=False)
score, align_human, align_fruitfly = compute_local_alignment(
seq_x=human_protein,
seq_y=fruitfly_protein,
scoring_matrix=scoring_matrix,
alignment_matrix=alignment_matrix)
return score, align_human, align_fruitfly
