def test01(self):
alphabet= "ACTG"
matrix = build_scoring_matrix(alphabet, 10,4,-2)
self.assertEquals(matrix['-']['-'],-2)
self.assertEquals(matrix['A']['A'],10)
self.assertEquals(matrix['C']['A'],4)
def test01(self):
alphabet = "ACTG"
matrix = build_scoring_matrix(alphabet, 10, 4, -2)
self.assertEquals(matrix['-']['-'], -2)
self.assertEquals(matrix['A']['A'], 10)
self.assertEquals(matrix['C']['A'], 4)
def check_spelling(checked_word, dist, words):
mispelled = []
scoring_matrix = build_scoring_matrix(string.ascii_lowercase, 2, 1, 0)
for word in words:
if calculate_distance(checked_word, word, scoring_matrix) <= dist:
mispelled.append(word)
return mispelled
def test01(self):
alphabet= "ACTG"
matrix = build_scoring_matrix(alphabet, 10,4,-2)
S = compute_alignment_matrix("AA", "TAAT", matrix, True)
(score,x,y) = compute_global_alignment("AA", "TAAT", matrix, S)
self.assertEqual(score,16)
self.assertEquals(x,"-AA-")
self.assertEquals(y,"TAAT")
def testGlobal(self):
alphabet= "ACTG"
matrix = build_scoring_matrix(alphabet, 10,4,-2)
S = compute_alignment_matrix("AA", "TAAT", matrix, True)
self.assertEquals(S[0][0], 0)
self.assertLess(S[0][1], 0)
self.assertLess(S[1][0], 0)
self.assertEquals(S[2][3],18)
def test01(self):
alphabet = "ACTG"
matrix = build_scoring_matrix(alphabet, 10, 4, -2)
S = compute_alignment_matrix("AA", "TAAT", matrix, True)
(score, x, y) = compute_local_alignment("AA", "TAAT", matrix, S)
self.assertEqual(score, 20)
self.assertEquals(x, "AA")
self.assertEquals(y, "AA")
def testGlobal(self):
alphabet = "ACTG"
matrix = build_scoring_matrix(alphabet, 10, 4, -2)
S = compute_alignment_matrix("AA", "TAAT", matrix, True)
self.assertEquals(S[0][0], 0)
self.assertLess(S[0][1], 0)
self.assertLess(S[1][0], 0)
self.assertEquals(S[2][3], 18)
# coding: utf-8
# In[32]:
import seq_align
from Bio import SeqIO, Seq
# In[22]:
score_mat = seq_align.build_scoring_matrix(set(["A", "T", "G", "C"]), 10, -10, 0)
# In[33]:
seq_recs = SeqIO.parse("/Users/richard/Downloads/rosalind_lcsq.txt", "fasta")
seq_x, seq_y = [str(seq.seq) for seq in seq_recs]
# In[34]:
align_mat = seq_align.compute_alignment_matrix(seq_x, seq_y, score_mat, True)
# In[35]:
_, align1, align2 = seq_align.compute_global_alignment(seq_x, seq_y, score_mat, align_mat)
print align1
print align2
