From 1953baa1980d7b5cc8881927cc4db00799e957c6 Mon Sep 17 00:00:00 2001
From: Samuel Ortion <samuel+git@ortion.fr>
Date: Fri, 29 Mar 2024 10:05:13 +0100
Subject: [PATCH] fix: Use correct backtrack algo
MIME-Version: 1.0
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Co-authored-by: Naïa Périnelle <naia.perinelle@laposte.net>
---
 figures/part2/needle-backtrack-stack.lua |  22 +++
 figures/part2/needle.lua                 | 195 +++++++++++++++++++++++
 figures/part2/needle.pdf                 |   3 +
 figures/part2/needle.tex                 |  20 +++
 4 files changed, 240 insertions(+)
 create mode 100644 figures/part2/needle-backtrack-stack.lua
 create mode 100755 figures/part2/needle.lua
 create mode 100644 figures/part2/needle.pdf
 create mode 100755 figures/part2/needle.tex

diff --git a/figures/part2/needle-backtrack-stack.lua b/figures/part2/needle-backtrack-stack.lua
new file mode 100644
index 0000000..e23e2fd
--- /dev/null
+++ b/figures/part2/needle-backtrack-stack.lua
@@ -0,0 +1,22 @@
+needle = require("./needle")
+
+function multiple_path_backtrack_trace(matrix, seq1, seq2)
+    local stack = {}
+    local m=string.len(seq1)
+    local n=string.len(seq2)
+    local i=m
+    local j=n
+    table.insert(1, {i, j, nil})
+    while #stack ~= 0 do
+        local state = table.remove(stack, 1)
+        local i=state[1]
+        local j=state[2]
+        local alignment = state[3]
+    end
+end
+
+function main()
+    local seq1 = "ATCTGAT"
+    local seq2 = "TGCATA"
+    local matrix = needle.needle_matrix(seq1, seq2)
+end
diff --git a/figures/part2/needle.lua b/figures/part2/needle.lua
new file mode 100755
index 0000000..c819bce
--- /dev/null
+++ b/figures/part2/needle.lua
@@ -0,0 +1,195 @@
+gap_penalty = 1
+mismatch_penalty = 1
+match_penalty = 0
+
+function needle_matrix(seq1, seq2)
+
+    local n1 = string.len(seq1)
+    local n2 = string.len(seq2)
+    -- Create a n1 x n2 matrix
+    local matrix = {}
+    for i=0,n1 do
+        matrix[i] = {}
+        for j=0,n2 do
+            matrix[i][j] = 0
+        end
+    end
+    -- Fill first row and first column
+    for i=1,n1 do
+        matrix[i][0] = i * gap_penalty
+    end
+    for i=1,n2 do
+        matrix[0][i] = i * gap_penalty
+    end
+    -- Fill the rest of the matrix
+    local match, delete, insert
+    for i=1,n1 do
+        for j=1,n2 do
+            if string.sub(seq1, i, i) == string.sub(seq2, j, j) then
+                match = matrix[i-1][j-1] + match_penalty
+            else
+                match = matrix[i-1][j-1] + mismatch_penalty
+            end
+            delete = matrix[i-1][j] + gap_penalty
+            insert = matrix[i][j-1] + gap_penalty
+            matrix[i][j] = math.min(match, delete, insert)
+        end
+    end
+    return matrix
+end
+
+function draw_needle_matrix(seq1, seq2)
+    -- tex.print(string.format(" Path: %s -> %s", seq1, seq2))
+    matrix = needle_matrix(seq1, seq2)
+    n1 = string.len(seq1)
+    n2 = string.len(seq2)
+    -- Draw the matrix as tikz nodes
+    for i=0,n1-1 do
+        for j=0,n2-1 do
+            tex.print(string.format("\\node[draw, minimum width=1cm, minimum height=1cm] at (%d, -%d) {};", i, j, matrix[i][j]))
+        end
+    end
+    -- Draw the sequence labels
+    for i=1,n1 do
+        tex.print(string.format("\\node at (%d, -%d) {%s};", i-1, -1, string.sub(seq1, i, i)))
+    end
+    for i=1,n2 do
+        tex.print(string.format("\\node at (%d, -%d) {%s};", -1, i-1, string.sub(seq2, i, i)))
+    end
+    -- Add a path from the bottom right corner to the top left corner, following the minimum of the three possible moves at each step
+    local i, j, value, previous_value
+    i = n1-1
+    j = n2-1
+    tex.print(string.format("\\draw[-,line width=2, gray] (%d, -%d) --", i, j))
+    while i > 0 and j > 0 do
+        value = math.min(matrix[i-1][j-1], table[i-1][j], table[i][j-1])
+        if value == matrix[i-1][j-1] then
+            i = i - 1
+            j = j - 1
+        elseif value == matrix[i-1][j] then
+            i = i - 1
+        else
+            j = j - 1
+        end
+        tex.print(string.format(" (%d, -%d) -- ", i, j))
+    end
+    tex.print(string.format("(0, 0) -- (-1, 1);", i, j))
+end
+
+local function has_value (tab, val)
+    for index, value in ipairs(tab) do
+        if value == val then
+            return true
+        end
+    end
+
+    return false
+end
+
+function sub(a, b)
+    if (a==b) then
+        return match_penalty
+    else
+        return mismatch_penalty
+    end
+end
+
+-- Returns true if it could have passed from k, l, to i, j
+-- during dynamic programming matrix building
+function check_path(matrix, i, j, k, l, seq1, seq2)
+    -- diagonal
+    if ((i == k + 1) and (j == l + 1)) then
+        if (matrix[i][j] == matrix[k][l] + sub(string.sub(seq1, i, i), string.sub(seq2, j, j))) then
+            return true
+        end
+    elseif (matrix[i][j] == matrix[k][l] + 1) then
+        return true
+    end
+    return false
+end
+
+function draw_needle_matrix_graph(seq1, seq2)
+    local matrix = needle_matrix(seq1, seq2)
+    local tikz_code = ""
+    function coordinate(i, j)
+        return i .. "_" .. j
+    end
+    local steps = {
+        {-1, -1},
+        {-1, 0},
+        {0, -1}
+    }
+
+    local n1 = string.len(seq1)
+    local n2 = string.len(seq2)
+    local path = {}
+    local i = n1
+    local j = n2
+    while i >= 0 and j >= 0 do
+        path[#path+1] = coordinate(i, j)
+        local min = matrix[i][j]
+        local min_step = steps[1]
+        for index, step in ipairs(steps) do
+            local k = i + step[1]
+            local l = j + step[2]
+            if k >= 0 and l >= 0 and check_path(matrix, i, j, k, l, seq1, seq2) then
+                min_step = step
+                min = matrix[k][l]
+                break
+            end
+        end
+        i = i + min_step[1]
+        j = j + min_step[2]
+--         print(i, j)
+    end
+    -- Draw the matrix as tikz node with matrix value
+    for i=0,n1 do
+        for j=0,n2 do
+            local options = ""
+            if has_value(path, coordinate(i, j)) then
+                options = "[fill=gray, draw, minimum size=1]"
+            end
+            tikz_code = tikz_code .. "\\node" .. options .. " (" .. coordinate(i, j) .. ") at (" .. i .. ", " .. -j .. ")" .. " {" .. matrix[i][j] .. "};"
+        end
+    end
+    -- Add nucleotide labels
+    for i=1,n1 do
+        local nt = string.sub(seq1, i, i)
+        tikz_code = tikz_code .. "\\node at (".. i .. "," .. 1 .. ")" .. "{$" .. nt .."$};"
+    end
+    for i=1,n2 do
+        local nt = string.sub(seq2, i, i)
+        tikz_code = tikz_code .. "\\node at (" .. -1 .. ", " .. -i .. ")" .. "{$ ".. nt .."$};"
+    end
+    -- For seq2
+       for i=0,n1 do
+        for j=0,n2 do
+            local min = math.huge
+            for index, step in ipairs(steps) do
+                local k = i + step[1]
+                local l = j + step[2]
+                if k >= 0 and l >= 0 and matrix[k][l] < min then
+                    min = matrix[k][l]
+                end
+            end
+--             local highlighted = false
+            for index, step in ipairs(steps) do
+                local k = i + step[1]
+                local l = j + step[2]
+                if k >= 0 and l >= 0 and check_path(matrix, i, j, k, l, seq1, seq2) then
+                    tikz_code = tikz_code .. "\\draw[->] (" .. coordinate(i, j) .. ")" .. " -- " .. "(" .. coordinate (k, l) .. ");"
+                end
+            end
+        end
+    end
+    return tikz_code
+end
+
+-- print(draw_needle_matrix_graph("ATGC", "TAGCGA"))
+
+return {
+  draw=draw_needle_matrix_graph,
+  gap_penalty=gap_penalty,
+  mismatch_penalty=mismatch_penalty,
+  match_penalty=match_penalty
+}
diff --git a/figures/part2/needle.pdf b/figures/part2/needle.pdf
new file mode 100644
index 0000000..c032ef7
--- /dev/null
+++ b/figures/part2/needle.pdf
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a190228082d5d244929900a3dd22ba34f727ea1aae9226362f421a7670741416
+size 14729
diff --git a/figures/part2/needle.tex b/figures/part2/needle.tex
new file mode 100755
index 0000000..b7a2d75
--- /dev/null
+++ b/figures/part2/needle.tex
@@ -0,0 +1,20 @@
+\documentclass[tikz]{standalone}
+
+\usepackage{luacode}
+\usepackage{tikz}
+
+\begin{document}
+
+\begin{tikzpicture}
+  \newcommand{\seqone}{TGCATA}
+  \newcommand{\seqtwo}{ATCTGAT}
+  \begin{luacode}
+    local needle = require("needle")
+    seq1 = \luastring{\seqone}
+    seq2 = \luastring{\seqtwo}
+    local tikz_code = needle.draw(seq1, seq2)
+    tex.print(tikz_code)
+  \end{luacode}
+\end{tikzpicture}
+
+\end{document}