9108ce75f1
Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1 Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984
147 lines
3.2 KiB
Awk
147 lines
3.2 KiB
Awk
#
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# NWS alignment
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#
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# -----------------------
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# make identity substitution matrix for given alphabet
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#
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function IdentityMatrix(alpha, mat, diag, ndiag, _local_, n, i, j, ci, cj) {
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if (diag == "") diag = 0
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if (ndiag == "") ndiag = 1
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alpha = toupper(alpha)
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delete mat
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n = length(alpha)
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for (i = 1 ; i <= n ; i++) {
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ci = substr(alpha, i, 1)
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for (j = 1 ; j <= n ; j++) {
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cj = substr(alpha, j, 1)
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mat[ci][cj] = (i == j) ? diag : ndiag
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}
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}
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}
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# -----------------------
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# internal utility : reverse string
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#
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function _Reverse(s, _local_, i, n, rs) {
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rs = "";
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n = length(s);
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for (i = n ; i >= 1 ; i--)
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rs = rs "" substr(s, i, 1)
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return rs;
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}
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# -----------------------
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# internal utility : alignment traceback for NWS
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#
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function _Traceback(dir, s1, s2, n1, n2, align, _local_, i, c1, c2, c3) {
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delete align
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while (dir[n1][n2] != 0) {
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if (dir[n1][n2] == "s") {
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c1 = substr(s1, n1--, 1)
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c2 = substr(s2, n2--, 1)
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c3 = (c1 == c2) ? tolower(c1) : "*"
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}
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else if (dir[n1][n2] == "i") {
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c1 = "-"
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c2 = substr(s2, n2--, 1)
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c3 = "-"
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}
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else {
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c1 = substr(s1, n1--, 1)
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c2 = "-"
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c3 = "-"
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}
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align[1] = align[1] "" c1
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align[2] = align[2] "" c2
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align[3] = align[3] "" c3
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}
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for (i = 1 ; i <= 3 ; i++)
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align[i] = _Reverse(align[i])
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}
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# -----------------------
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# internal utility : min
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#
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function _Min(a, b) {
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return (a < b ? a : b)
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}
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# -----------------------
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# sequence alignment NWS
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#
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# todo : check alphabet
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#
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# --> i
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# |
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# v d
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#
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function AlignNWS(s1, s2, subst, indel, local, align,
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_local_, rev, n1, n2, i, j, c1, c2, m2,
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ws, wi, wd, w,
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mat, dir) {
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s1 = toupper(s1) ; s2 = toupper(s2)
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n1 = length(s1) ; n2 = length(s2)
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if (local && (n2 < n1)) {
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rev = s1 ; s1 = s2 ; s2 = rev
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rev = n1 ; n1 = n2 ; n2 = rev
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}
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if (indel == "") indel = 1
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#
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# nws alignment
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#
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for (i = 0 ; i <= n1 ; i++) {
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c1 = substr(s1, i, 1)
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for (j = 0 ; j <= n2 ; j++) {
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c2 = substr(s2, j, 1)
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if (i && j) {
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ws = mat[i-1][j-1] + subst[c1][c2]
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wd = mat[i-1][j] + indel
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wi = mat[i][j-1] + indel
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w = _Min(ws, _Min(wi, wd))
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mat[i][j] = w
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dir[i][j] = (w == ws) ? "s" : (w == wi) ? "i" : "d"
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} else if (i) {
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mat[i][j] = mat[i-1][j] + indel
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dir[i][j] = "d"
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} else if (j) {
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mat[i][j] = mat[i][j-1] + (local ? 0 : indel)
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dir[i][j] = "i"
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} else {
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mat[i][j] = 0
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dir[i][j] = 0
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}
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}
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# delete mat[i-1]
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}
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#
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# adjust last line in local mode
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#
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if (local) {
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m2 = n2
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for (j = m2 ; j >= 0 ; j--) {
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if (mat[n1][j] < mat[n1][m2])
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m2 = j
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}
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mat[n1][n2] = mat[n1][m2]
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for (j = m2 + 1 ; j <= n2 ; j++) {
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dir[n1][j] = "i"
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}
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}
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#
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# traceback
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#
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_Traceback(dir, s1, s2, n1, n2, align)
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if (rev) {
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rev = align[1] ; align[1] = align[2]; align[2] = rev
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}
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return mat[n1][n2]
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}
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