d77a0dfe67
Former-commit-id: 07fb256bf17db3f0ffc1730b0383f8255fbb9129 Former-commit-id: fd6a1fe72a39c5633c2f9fb6de09af979c2a48f3
147 lines
3.2 KiB
Awk
147 lines
3.2 KiB
Awk
#
|
|
# NWS alignment
|
|
#
|
|
|
|
# -----------------------
|
|
# make identity substitution matrix for given alphabet
|
|
#
|
|
function IdentityMatrix(alpha, mat, diag, ndiag, _local_, n, i, j, ci, cj) {
|
|
if (diag == "") diag = 0
|
|
if (ndiag == "") ndiag = 1
|
|
alpha = toupper(alpha)
|
|
delete mat
|
|
n = length(alpha)
|
|
for (i = 1 ; i <= n ; i++) {
|
|
ci = substr(alpha, i, 1)
|
|
for (j = 1 ; j <= n ; j++) {
|
|
cj = substr(alpha, j, 1)
|
|
mat[ci][cj] = (i == j) ? diag : ndiag
|
|
}
|
|
}
|
|
}
|
|
|
|
# -----------------------
|
|
# internal utility : reverse string
|
|
#
|
|
function _Reverse(s, _local_, i, n, rs) {
|
|
rs = "";
|
|
n = length(s);
|
|
for (i = n ; i >= 1 ; i--)
|
|
rs = rs "" substr(s, i, 1)
|
|
return rs;
|
|
}
|
|
|
|
# -----------------------
|
|
# internal utility : alignment traceback for NWS
|
|
#
|
|
function _Traceback(dir, s1, s2, n1, n2, align, _local_, i, c1, c2, c3) {
|
|
delete align
|
|
while (dir[n1][n2] != 0) {
|
|
if (dir[n1][n2] == "s") {
|
|
c1 = substr(s1, n1--, 1)
|
|
c2 = substr(s2, n2--, 1)
|
|
c3 = (c1 == c2) ? tolower(c1) : "*"
|
|
}
|
|
else if (dir[n1][n2] == "i") {
|
|
c1 = "-"
|
|
c2 = substr(s2, n2--, 1)
|
|
c3 = "-"
|
|
}
|
|
else {
|
|
c1 = substr(s1, n1--, 1)
|
|
c2 = "-"
|
|
c3 = "-"
|
|
}
|
|
align[1] = align[1] "" c1
|
|
align[2] = align[2] "" c2
|
|
align[3] = align[3] "" c3
|
|
}
|
|
for (i = 1 ; i <= 3 ; i++)
|
|
align[i] = _Reverse(align[i])
|
|
}
|
|
|
|
# -----------------------
|
|
# internal utility : min
|
|
#
|
|
function _Min(a, b) {
|
|
return (a < b ? a : b)
|
|
}
|
|
|
|
# -----------------------
|
|
# sequence alignment NWS
|
|
#
|
|
# todo : check alphabet
|
|
#
|
|
# --> i
|
|
# |
|
|
# v d
|
|
#
|
|
function AlignNWS(s1, s2, subst, indel, local, align,
|
|
_local_, rev, n1, n2, i, j, c1, c2, m2,
|
|
ws, wi, wd, w,
|
|
mat, dir) {
|
|
|
|
s1 = toupper(s1) ; s2 = toupper(s2)
|
|
n1 = length(s1) ; n2 = length(s2)
|
|
if (local && (n2 < n1)) {
|
|
rev = s1 ; s1 = s2 ; s2 = rev
|
|
rev = n1 ; n1 = n2 ; n2 = rev
|
|
}
|
|
|
|
if (indel == "") indel = 1
|
|
|
|
#
|
|
# nws alignment
|
|
#
|
|
for (i = 0 ; i <= n1 ; i++) {
|
|
c1 = substr(s1, i, 1)
|
|
for (j = 0 ; j <= n2 ; j++) {
|
|
c2 = substr(s2, j, 1)
|
|
if (i && j) {
|
|
ws = mat[i-1][j-1] + subst[c1][c2]
|
|
wd = mat[i-1][j] + indel
|
|
wi = mat[i][j-1] + indel
|
|
w = _Min(ws, _Min(wi, wd))
|
|
mat[i][j] = w
|
|
dir[i][j] = (w == ws) ? "s" : (w == wi) ? "i" : "d"
|
|
} else if (i) {
|
|
mat[i][j] = mat[i-1][j] + indel
|
|
dir[i][j] = "d"
|
|
} else if (j) {
|
|
mat[i][j] = mat[i][j-1] + (local ? 0 : indel)
|
|
dir[i][j] = "i"
|
|
} else {
|
|
mat[i][j] = 0
|
|
dir[i][j] = 0
|
|
}
|
|
}
|
|
# delete mat[i-1]
|
|
}
|
|
|
|
#
|
|
# adjust last line in local mode
|
|
#
|
|
if (local) {
|
|
m2 = n2
|
|
for (j = m2 ; j >= 0 ; j--) {
|
|
if (mat[n1][j] < mat[n1][m2])
|
|
m2 = j
|
|
}
|
|
mat[n1][n2] = mat[n1][m2]
|
|
for (j = m2 + 1 ; j <= n2 ; j++) {
|
|
dir[n1][j] = "i"
|
|
}
|
|
}
|
|
|
|
#
|
|
# traceback
|
|
#
|
|
_Traceback(dir, s1, s2, n1, n2, align)
|
|
|
|
if (rev) {
|
|
rev = align[1] ; align[1] = align[2]; align[2] = rev
|
|
}
|
|
|
|
return mat[n1][n2]
|
|
}
|