fix: Use correct backtrack algo
Co-authored-by: Naïa Périnelle <naia.perinelle@laposte.net>
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@ -0,0 +1,22 @@
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needle = require("./needle")
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function multiple_path_backtrack_trace(matrix, seq1, seq2)
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local stack = {}
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local m=string.len(seq1)
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local n=string.len(seq2)
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local i=m
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local j=n
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table.insert(1, {i, j, nil})
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while #stack ~= 0 do
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local state = table.remove(stack, 1)
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local i=state[1]
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local j=state[2]
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local alignment = state[3]
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end
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end
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function main()
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local seq1 = "ATCTGAT"
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local seq2 = "TGCATA"
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local matrix = needle.needle_matrix(seq1, seq2)
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end
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@ -0,0 +1,195 @@
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gap_penalty = 1
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mismatch_penalty = 1
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match_penalty = 0
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function needle_matrix(seq1, seq2)
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local n1 = string.len(seq1)
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local n2 = string.len(seq2)
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-- Create a n1 x n2 matrix
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local matrix = {}
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for i=0,n1 do
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matrix[i] = {}
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for j=0,n2 do
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matrix[i][j] = 0
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end
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end
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-- Fill first row and first column
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for i=1,n1 do
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matrix[i][0] = i * gap_penalty
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end
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for i=1,n2 do
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matrix[0][i] = i * gap_penalty
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end
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-- Fill the rest of the matrix
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local match, delete, insert
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for i=1,n1 do
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for j=1,n2 do
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if string.sub(seq1, i, i) == string.sub(seq2, j, j) then
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match = matrix[i-1][j-1] + match_penalty
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else
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match = matrix[i-1][j-1] + mismatch_penalty
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end
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delete = matrix[i-1][j] + gap_penalty
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insert = matrix[i][j-1] + gap_penalty
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matrix[i][j] = math.min(match, delete, insert)
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end
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end
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return matrix
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end
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function draw_needle_matrix(seq1, seq2)
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-- tex.print(string.format(" Path: %s -> %s", seq1, seq2))
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matrix = needle_matrix(seq1, seq2)
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n1 = string.len(seq1)
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n2 = string.len(seq2)
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-- Draw the matrix as tikz nodes
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for i=0,n1-1 do
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for j=0,n2-1 do
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tex.print(string.format("\\node[draw, minimum width=1cm, minimum height=1cm] at (%d, -%d) {};", i, j, matrix[i][j]))
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end
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end
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-- Draw the sequence labels
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for i=1,n1 do
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tex.print(string.format("\\node at (%d, -%d) {%s};", i-1, -1, string.sub(seq1, i, i)))
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end
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for i=1,n2 do
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tex.print(string.format("\\node at (%d, -%d) {%s};", -1, i-1, string.sub(seq2, i, i)))
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end
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-- Add a path from the bottom right corner to the top left corner, following the minimum of the three possible moves at each step
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local i, j, value, previous_value
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i = n1-1
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j = n2-1
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tex.print(string.format("\\draw[-,line width=2, gray] (%d, -%d) --", i, j))
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while i > 0 and j > 0 do
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value = math.min(matrix[i-1][j-1], table[i-1][j], table[i][j-1])
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if value == matrix[i-1][j-1] then
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i = i - 1
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j = j - 1
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elseif value == matrix[i-1][j] then
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i = i - 1
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else
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j = j - 1
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end
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tex.print(string.format(" (%d, -%d) -- ", i, j))
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end
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tex.print(string.format("(0, 0) -- (-1, 1);", i, j))
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end
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local function has_value (tab, val)
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for index, value in ipairs(tab) do
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if value == val then
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return true
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end
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end
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return false
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end
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function sub(a, b)
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if (a==b) then
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return match_penalty
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else
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return mismatch_penalty
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end
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end
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-- Returns true if it could have passed from k, l, to i, j
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-- during dynamic programming matrix building
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function check_path(matrix, i, j, k, l, seq1, seq2)
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-- diagonal
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if ((i == k + 1) and (j == l + 1)) then
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if (matrix[i][j] == matrix[k][l] + sub(string.sub(seq1, i, i), string.sub(seq2, j, j))) then
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return true
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end
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elseif (matrix[i][j] == matrix[k][l] + 1) then
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return true
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end
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return false
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end
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function draw_needle_matrix_graph(seq1, seq2)
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local matrix = needle_matrix(seq1, seq2)
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local tikz_code = ""
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function coordinate(i, j)
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return i .. "_" .. j
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end
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local steps = {
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{-1, -1},
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{-1, 0},
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{0, -1}
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}
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local n1 = string.len(seq1)
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local n2 = string.len(seq2)
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local path = {}
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local i = n1
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local j = n2
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while i >= 0 and j >= 0 do
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path[#path+1] = coordinate(i, j)
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local min = matrix[i][j]
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local min_step = steps[1]
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for index, step in ipairs(steps) do
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local k = i + step[1]
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local l = j + step[2]
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if k >= 0 and l >= 0 and check_path(matrix, i, j, k, l, seq1, seq2) then
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min_step = step
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min = matrix[k][l]
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break
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end
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end
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i = i + min_step[1]
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j = j + min_step[2]
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-- print(i, j)
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end
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-- Draw the matrix as tikz node with matrix value
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for i=0,n1 do
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for j=0,n2 do
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local options = ""
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if has_value(path, coordinate(i, j)) then
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options = "[fill=gray, draw, minimum size=1]"
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end
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tikz_code = tikz_code .. "\\node" .. options .. " (" .. coordinate(i, j) .. ") at (" .. i .. ", " .. -j .. ")" .. " {" .. matrix[i][j] .. "};"
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end
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end
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-- Add nucleotide labels
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for i=1,n1 do
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local nt = string.sub(seq1, i, i)
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tikz_code = tikz_code .. "\\node at (".. i .. "," .. 1 .. ")" .. "{$" .. nt .."$};"
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end
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for i=1,n2 do
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local nt = string.sub(seq2, i, i)
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tikz_code = tikz_code .. "\\node at (" .. -1 .. ", " .. -i .. ")" .. "{$ ".. nt .."$};"
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end
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-- For seq2
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for i=0,n1 do
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for j=0,n2 do
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local min = math.huge
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for index, step in ipairs(steps) do
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local k = i + step[1]
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local l = j + step[2]
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if k >= 0 and l >= 0 and matrix[k][l] < min then
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min = matrix[k][l]
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end
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end
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-- local highlighted = false
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for index, step in ipairs(steps) do
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local k = i + step[1]
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local l = j + step[2]
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if k >= 0 and l >= 0 and check_path(matrix, i, j, k, l, seq1, seq2) then
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tikz_code = tikz_code .. "\\draw[->] (" .. coordinate(i, j) .. ")" .. " -- " .. "(" .. coordinate (k, l) .. ");"
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end
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end
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end
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end
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return tikz_code
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end
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-- print(draw_needle_matrix_graph("ATGC", "TAGCGA"))
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return {
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draw=draw_needle_matrix_graph,
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gap_penalty=gap_penalty,
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mismatch_penalty=mismatch_penalty,
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match_penalty=match_penalty
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}
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Binary file not shown.
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@ -0,0 +1,20 @@
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\documentclass[tikz]{standalone}
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\usepackage{luacode}
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\usepackage{tikz}
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\begin{document}
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\begin{tikzpicture}
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\newcommand{\seqone}{TGCATA}
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\newcommand{\seqtwo}{ATCTGAT}
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\begin{luacode}
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local needle = require("needle")
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seq1 = \luastring{\seqone}
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seq2 = \luastring{\seqtwo}
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local tikz_code = needle.draw(seq1, seq2)
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tex.print(tikz_code)
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\end{luacode}
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\end{tikzpicture}
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\end{document}
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