Newer
Older
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 15 15:02:16 2019
@author: ariane.delrocq
"""
import Bio.SubsMat.MatrixInfo
import Bio.SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
import Bio.pairwise2
seqs=[]
handle = open("balibase/RV11.unaligned/BBS11001.fasta")
for seq in Bio.SeqIO.parse(handle, "fasta"):
seqs.append(seq)
handle.close()
mat = Bio.SubsMat.MatrixInfo.blosum62
def score(a, b, gap=-8, id=1, mut=-1):
if not a or not b:
return gap
else:
a = a.upper()
b = b.upper()
try:
return mat[a,b]
except KeyError:
return mat[b,a]
# elif a==b:
# return id
# else:
# return mut
def align(seq1, seq2):
x = seq1.seq
y = seq2.seq
mm = [[0 for _ in range(m+1)] for _ in range(n+1)] # scores matrix
path = [[0 for _ in range(m+1)] for _ in range(n+1)] # last step for optimal score
# first line and col
for i in range(1, n+1):
mm[i][0] = mm[i-1][0] + score('', x[i-1])
mm[0][j] = mm[j-1][0] + score('', y[j-1])
path[0][j] = (0, j-1)
# fill table
for i in range(1, n+1):
for j in range(1, m+1):
a = x[i-1]
b = y[j-1]
s1 = mm[i-1][j-1] + score(a,b)
s2 = mm[i-1][j] + score('', a)
s3 = mm[i][j-1] + score('', b)
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
bestScore = mm[n][m]
alx = ""
aly = ""
i, j = n, m
while i > 0 and j > 0:
i2, j2 = path[i][j]
if i==i2:
alx+='-'
else:
alx+=x[i-1]
if j==j2:
aly+='-'
else:
aly+=y[j-1]
i,j = i2, j2
while i>0:
aly+='-'
alx+=x[i-1]
i -=1
while j>0:
alx+='-'
aly+=y[j-1]
j -=1
alx = alx[::-1]
aly = aly[::-1]
seq1.seq = Seq(alx)
seq2.seq = Seq(aly)
return bestScore, seq1, seq2
def align2steps(seq1, seq2, d=8, e=4):
x = seq1.seq
y = seq2.seq
n=len(x)
m=len(y)
mm = [[0 for _ in range(m+1)] for _ in range(n+1)] # scores matrix
mx = [[0 for _ in range(m+1)] for _ in range(n+1)]
my = [[0 for _ in range(m+1)] for _ in range(n+1)]
pathm = [[0 for _ in range(m+1)] for _ in range(n+1)] # last step for optimal score
pathx = [[0 for _ in range(m+1)] for _ in range(n+1)]
pathy = [[0 for _ in range(m+1)] for _ in range(n+1)]
lower_bound = - (n+m) * max(e,d)
# first line and col
for i in range(1, n+1):
mx[i][0] = -d -(i-1)*e
pathx[i][0] = pathx
# Best alignment ending with no gap but with 0 letters of one seq does
# not exist... but is still used in the formulas below
mm[i][0] = lower_bound
# Same for best alignment with 0 letter of Y ending on a gap on the X
# side with a letter of Y
my[i][0] = lower_bound
my[0][j] = -d - (j-1)*e
pathy[0][j] = pathy
mm[0][j] = lower_bound
mx[0][j] = lower_bound
for i in range(1, n+1):
for j in range(1, m+1):
a = x[i-1]
b = y[j-1]
# find max for M
s1 = mm[i-1][j-1] + score(a,b)
s2 = mx[i-1][j-1] + score(a,b)
if s1 >= s2:
if s1 >= s3:
mm[i][j] = s1
else: # s2 > s1
if s2 >= s3:
mm[i][j] = s2
# find max for I_x
s4 = mm[i-1][j] - d
s5 = mx[i-1][j] - e
if s4 >= s5:
mx[i][j] = s4
# find max for I_y
s6 = mm[i][j-1] - d
s7 = my[i][j-1] - e
if s6 >= s7:
my[i][j] = s6
pathy[i][j] = pathy
bestScore, bestPath = max(
[(mm,pathm),(mx,pathx),(my,pathy)],
key=(lambda t:t[0][n][m]))
bestScore = bestScore[n][m]
prev_path = path[i][j]
if path == pathm:
i -= 1
j -= 1
alx += x[i]
aly += y[j]
elif path == pathy:
j -= 1
alx += '-'
aly += y[j]
i -= 1
alx += x[i]
aly += '-'
path = prev_path
while i>0:
aly+='-'
alx+=x[i-1]
i -=1
while j>0:
alx+='-'
aly+=y[j-1]
j -=1
alx = alx[::-1]
aly = aly[::-1]
aseq1 = SeqRecord(seq1)
aseq1.seq = Seq(alx)
aseq2 = SeqRecord(seq2)
aseq2.seq = Seq(aly)
return bestScore, aseq1, aseq2
def test():
# print(align("chat", "cat"))
# print(align("chat", "cgat"))
# print(align("chat", "at"))
s, x, y = align2steps(seqs[0], seqs[1])
print(s)
print(x.seq)
print(y.seq)
with open("balibase/us/1.fasta", "w") as fd:
Bio.SeqIO.write((x, y), fd, "fasta")
print("Ref:")
ref = Bio.pairwise2.align.globalds(
seqs[0].seq, seqs[1].seq,
Bio.SubsMat.MatrixInfo.blosum62, -8, -4)
for x, y, s, *_ in ref:
print(s)
print(x)
print(y)