def test_compute_local_alignment():
"""
Test the function compute_global_alignment function
"""
suite = poc_simpletest.TestSuite()
scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 4, -6)
alignment_matrix = proj4_solution.compute_alignment_matrix("AA", "TAAT", scoring_matrix, False)
local_alignment_sequence = proj4_solution.compute_local_alignment("AA", "TAAT", scoring_matrix, alignment_matrix)
print local_alignment_sequence
suite.run_test(local_alignment_sequence, (20, "AA", "AA"), "Error Found")
scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 2, -4)
alignment_matrix = proj4_solution.compute_alignment_matrix("---AC-C--", "TTTACACGG", scoring_matrix, False)
local_alignment_sequence = proj4_solution.compute_local_alignment(
"---AC-C--", "TTTACACGG", scoring_matrix, alignment_matrix
)
print local_alignment_sequence
suite.run_test(local_alignment_sequence, (26, "AC-C", "ACAC"), "Error Found")
local_alignment_sequence = proj4_solution.compute_local_alignment(
"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},
"G": {"A": 2, "C": 2, "-": -4, "T": 2, "G": 6},
},
[[0, 0], [0, 6]],
)
print local_alignment_sequence
suite.run_test(local_alignment_sequence, (6, "A", "A"), "Error Found")
suite.report_results()
def test_compute_local_alignment():
"""
Test the function compute_global_alignment function
"""
suite = poc_simpletest.TestSuite()
scoring_matrix = proj4_solution.build_scoring_matrix(
set(['A', 'C', 'T', 'G']), 10, 4, -6)
alignment_matrix = proj4_solution.compute_alignment_matrix(
'AA', 'TAAT', scoring_matrix, False)
local_alignment_sequence = proj4_solution.compute_local_alignment(
'AA', 'TAAT', scoring_matrix, alignment_matrix)
print local_alignment_sequence
suite.run_test(local_alignment_sequence, (20, 'AA', 'AA'), "Error Found")
scoring_matrix = proj4_solution.build_scoring_matrix(
set(['A', 'C', 'T', 'G']), 10, 2, -4)
alignment_matrix = proj4_solution.compute_alignment_matrix(
'---AC-C--', 'TTTACACGG', scoring_matrix, False)
local_alignment_sequence = proj4_solution.compute_local_alignment(
'---AC-C--', 'TTTACACGG', scoring_matrix, alignment_matrix)
print local_alignment_sequence
suite.run_test(local_alignment_sequence, (26, 'AC-C', 'ACAC'),
"Error Found")
local_alignment_sequence = proj4_solution.compute_local_alignment(
'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
},
'G': {
'A': 2,
'C': 2,
'-': -4,
'T': 2,
'G': 6
}
}, [[0, 0], [0, 6]])
print local_alignment_sequence
suite.run_test(local_alignment_sequence, (6, 'A', 'A'), "Error Found")
suite.report_results()
def test_compute_global_alignment():
"""
Test the function compute_global_alignment function
"""
suite = poc_simpletest.TestSuite()
scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 4, -6)
alignment_matrix = proj4_solution.compute_alignment_matrix("AA", "TAAT", scoring_matrix, True)
global_alignment_sequence = proj4_solution.compute_global_alignment("AA", "TAAT", scoring_matrix, alignment_matrix)
print global_alignment_sequence
suite.run_test(global_alignment_sequence, (8, "-AA-", "TAAT"), "Error Found")
global_alignment_sequence = proj4_solution.compute_global_alignment(
"ACTACT",
"AGCTA",
{
"A": {"A": 2, "C": 1, "-": 0, "T": 1, "G": 1},
"C": {"A": 1, "C": 2, "-": 0, "T": 1, "G": 1},
"-": {"A": 0, "C": 0, "-": 0, "T": 0, "G": 0},
"T": {"A": 1, "C": 1, "-": 0, "T": 2, "G": 1},
"G": {"A": 1, "C": 1, "-": 0, "T": 1, "G": 2},
},
[
[0, 0, 0, 0, 0, 0],
[0, 2, 2, 2, 2, 2],
[0, 2, 3, 4, 4, 4],
[0, 2, 3, 4, 6, 6],
[0, 2, 3, 4, 6, 8],
[0, 2, 3, 5, 6, 8],
[0, 2, 3, 5, 7, 8],
],
)
print global_alignment_sequence
suite.run_test(global_alignment_sequence, (8, "A-CTACT", "AGCTA--"), "Error Found")
global_alignment_sequence = proj4_solution.compute_global_alignment(
"ACTACT",
"GGACTGCTTCTGG",
{
"A": {"A": 2, "C": 1, "-": 0, "T": 1, "G": 1},
"C": {"A": 1, "C": 2, "-": 0, "T": 1, "G": 1},
"-": {"A": 0, "C": 0, "-": 0, "T": 0, "G": 0},
"T": {"A": 1, "C": 1, "-": 0, "T": 2, "G": 1},
"G": {"A": 1, "C": 1, "-": 0, "T": 1, "G": 2},
},
[
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4],
[0, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6],
[0, 1, 2, 4, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7],
[0, 1, 2, 4, 6, 6, 7, 9, 9, 9, 9, 9, 9, 9],
[0, 1, 2, 4, 6, 8, 8, 9, 11, 11, 11, 11, 11, 11],
],
)
print global_alignment_sequence
suite.run_test(global_alignment_sequence, (11, "--A---CTACT--", "GGACTGCTTCTGG"), "Error Found")
suite.report_results()
def compute_edit_distance(word1, word2, scoring_matrix):
"""
Question 7
:return: The edit_distance between word1 and word2
"""
alignment_matrix = student.compute_alignment_matrix(word1, word2, scoring_matrix, True)
global_score = alignment_matrix[len(word1)][len(word2)]
edit_distance = len(word1) + len(word2) - global_score
return edit_distance
def compute_edit_distance(word1, word2, scoring_matrix):
"""
Question 7
:return: The edit_distance between word1 and word2
"""
alignment_matrix = student.compute_alignment_matrix(
word1, word2, scoring_matrix, True)
global_score = alignment_matrix[len(word1)][len(word2)]
edit_distance = len(word1) + len(word2) - global_score
return edit_distance
def local_alignment_eyeless_protein():
"""
Question: 1
"""
human_eyeless_seq = provided.read_protein(provided.HUMAN_EYELESS_URL)
fruitfly_eyeless_seq = provided.read_protein(provided.FRUITFLY_EYELESS_URL)
scoring_matrix = provided.read_scoring_matrix(provided.PAM50_URL)
alignment_matrix = student.compute_alignment_matrix(human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, False)
local_alignment = student.compute_local_alignment(human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, alignment_matrix)
return local_alignment
def test_compute_alignment_matrix():
"""
Test the function compute_alignment_matrix function
"""
suite = poc_simpletest.TestSuite()
scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 4, -6)
global_alignment_matrix = proj4_solution.compute_alignment_matrix("AA", "TAAT", scoring_matrix, False)
print global_alignment_matrix
suite.run_test(global_alignment_matrix[1][2], 4, "Error Found")
suite.report_results()
def test_compute_alignment_matrix():
"""
Test the function compute_alignment_matrix function
"""
suite = poc_simpletest.TestSuite()
scoring_matrix = proj4_solution.build_scoring_matrix(
set(['A', 'C', 'T', 'G']), 10, 4, -6)
global_alignment_matrix = proj4_solution.compute_alignment_matrix(
'AA', 'TAAT', scoring_matrix, False)
print global_alignment_matrix
suite.run_test(global_alignment_matrix[1][2], 4, "Error Found")
suite.report_results()
def local_alignment_eyeless_protein():
"""
Question: 1
"""
human_eyeless_seq = provided.read_protein(provided.HUMAN_EYELESS_URL)
fruitfly_eyeless_seq = provided.read_protein(provided.FRUITFLY_EYELESS_URL)
scoring_matrix = provided.read_scoring_matrix(provided.PAM50_URL)
alignment_matrix = student.compute_alignment_matrix(
human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, False)
local_alignment = student.compute_local_alignment(human_eyeless_seq,
fruitfly_eyeless_seq,
scoring_matrix,
alignment_matrix)
return local_alignment
def generate_null_distribution(seq_x, seq_y, scoring_matrix, num_trials):
"""
Question: 4: Compute null distribution
"""
scoring_distribution = {}
for _ in range(num_trials):
rand_y = list(seq_y)
random.shuffle(rand_y)
rand_y = "".join(rand_y)
print _
alignment_matrix = student.compute_alignment_matrix(seq_x, rand_y, scoring_matrix, False)
max_score = max(map(max, alignment_matrix))
if scoring_distribution.has_key(max_score):
scoring_distribution[max_score] += 1
else:
scoring_distribution[max_score] = 1
return scoring_distribution
def generate_null_distribution(seq_x, seq_y, scoring_matrix, num_trials):
"""
Question: 4: Compute null distribution
"""
scoring_distribution = {}
for _ in range(num_trials):
rand_y = list(seq_y)
random.shuffle(rand_y)
rand_y = "".join(rand_y)
print _
alignment_matrix = student.compute_alignment_matrix(
seq_x, rand_y, scoring_matrix, False)
max_score = max(map(max, alignment_matrix))
if scoring_distribution.has_key(max_score):
scoring_distribution[max_score] += 1
else:
scoring_distribution[max_score] = 1
return scoring_distribution
def global_alignment_consensus():
"""
Question: 2
"""
ans_similar = []
local_alignments = local_alignment_eyeless_protein()
consensus_seq = provided.read_protein(provided.CONSENSUS_PAX_URL)
scoring_matrix = provided.read_scoring_matrix(provided.PAM50_URL)
for idx in range(1, 3):
seq_x = local_alignments[idx]
seq_x = seq_x.replace("-", "")
alignment_matrix = student.compute_alignment_matrix(seq_x, consensus_seq, scoring_matrix, True)
global_alignment = student.compute_global_alignment(seq_x, consensus_seq, scoring_matrix, alignment_matrix)
similar_count = 0
for letter1, letter2 in zip(global_alignment[1], global_alignment[2]):
if letter1 == letter2:
similar_count += 1
ans_similar.append(float(similar_count * 100) / len(global_alignment[1]))
return ans_similar
def global_alignment_consensus():
"""
Question: 2
"""
ans_similar = []
local_alignments = local_alignment_eyeless_protein()
consensus_seq = provided.read_protein(provided.CONSENSUS_PAX_URL)
scoring_matrix = provided.read_scoring_matrix(provided.PAM50_URL)
for idx in range(1, 3):
seq_x = local_alignments[idx]
seq_x = seq_x.replace("-", "")
alignment_matrix = student.compute_alignment_matrix(
seq_x, consensus_seq, scoring_matrix, True)
global_alignment = student.compute_global_alignment(
seq_x, consensus_seq, scoring_matrix, alignment_matrix)
similar_count = 0
for letter1, letter2 in zip(global_alignment[1], global_alignment[2]):
if letter1 == letter2:
similar_count += 1
ans_similar.append(
float(similar_count * 100) / len(global_alignment[1]))
return ans_similar
def test_compute_global_alignment():
"""
Test the function compute_global_alignment function
"""
suite = poc_simpletest.TestSuite()
scoring_matrix = proj4_solution.build_scoring_matrix(
set(['A', 'C', 'T', 'G']), 10, 4, -6)
alignment_matrix = proj4_solution.compute_alignment_matrix(
'AA', 'TAAT', scoring_matrix, True)
global_alignment_sequence = proj4_solution.compute_global_alignment(
'AA', 'TAAT', scoring_matrix, alignment_matrix)
print global_alignment_sequence
suite.run_test(global_alignment_sequence, (8, '-AA-', 'TAAT'),
"Error Found")
global_alignment_sequence = proj4_solution.compute_global_alignment(
'ACTACT', 'AGCTA', {
'A': {
'A': 2,
'C': 1,
'-': 0,
'T': 1,
'G': 1
},
'C': {
'A': 1,
'C': 2,
'-': 0,
'T': 1,
'G': 1
},
'-': {
'A': 0,
'C': 0,
'-': 0,
'T': 0,
'G': 0
},
'T': {
'A': 1,
'C': 1,
'-': 0,
'T': 2,
'G': 1
},
'G': {
'A': 1,
'C': 1,
'-': 0,
'T': 1,
'G': 2
}
}, [[0, 0, 0, 0, 0, 0], [0, 2, 2, 2, 2, 2], [0, 2, 3, 4, 4, 4],
[0, 2, 3, 4, 6, 6], [0, 2, 3, 4, 6, 8], [0, 2, 3, 5, 6, 8],
[0, 2, 3, 5, 7, 8]])
print global_alignment_sequence
suite.run_test(global_alignment_sequence, (8, 'A-CTACT', 'AGCTA--'),
"Error Found")
global_alignment_sequence = proj4_solution.compute_global_alignment(
'ACTACT', 'GGACTGCTTCTGG', {
'A': {
'A': 2,
'C': 1,
'-': 0,
'T': 1,
'G': 1
},
'C': {
'A': 1,
'C': 2,
'-': 0,
'T': 1,
'G': 1
},
'-': {
'A': 0,
'C': 0,
'-': 0,
'T': 0,
'G': 0
},
'T': {
'A': 1,
'C': 1,
'-': 0,
'T': 2,
'G': 1
},
'G': {
'A': 1,
'C': 1,
'-': 0,
'T': 1,
'G': 2
}
}, [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4],
[0, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6],
[0, 1, 2, 4, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7],
[0, 1, 2, 4, 6, 6, 7, 9, 9, 9, 9, 9, 9, 9],
[0, 1, 2, 4, 6, 8, 8, 9, 11, 11, 11, 11, 11, 11]])
print global_alignment_sequence
suite.run_test(global_alignment_sequence,
(11, '--A---CTACT--', 'GGACTGCTTCTGG'), "Error Found")
suite.report_results()