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rendu GREGOIRE GENET #12

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260 changes: 248 additions & 12 deletions BINF2025_TP4.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,7 @@
"nbformat_minor": 0,
"metadata": {
"colab": {
"provenance": [],
"authorship_tag": "ABX9TyOkaYHMV5kAI2JXjqDKbiVa",
"include_colab_link": true
"provenance": []
},
"kernelspec": {
"name": "python3",
Expand All @@ -19,8 +17,7 @@
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
"id": "view-in-github"
},
"source": [
"<a href=\"https://colab.research.google.com/github/pparutto/BINF2025_TP4/blob/main/BINF2025_TP4.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
Expand Down Expand Up @@ -118,13 +115,27 @@
" for i in range(N):\n",
" e_I[i,:] = np.array([float(e) for e in f.readline().rstrip().split(\",\")])\n",
"\n",
" return (T, e_M, e_I)"
" return (T, e_M, e_I)\n",
"seq = read_fasta(\"easy1.fasta\")\n",
"print(seq)"
],
"metadata": {
"id": "30qlDWTmQ47E"
"id": "30qlDWTmQ47E",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "649edeb0-0ce6-4730-f69e-5427407ccc44"
},
"execution_count": null,
"outputs": []
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"['EL---W', 'E-EL-W', 'EL-EE-', '--EEEW', 'EL---W']\n"
]
}
]
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -184,7 +195,16 @@
{
"cell_type": "code",
"source": [
"#Votre code ici"
"import numpy as np\n",
"def mark_columns(A, alpha):\n",
" P = len(A)\n",
" N = len(A[0])\n",
" marked = []\n",
" for j in range(N):\n",
" gap_count = sum(1 for i in range(P) if A[i][j] == '-')\n",
" if gap_count / P < alpha:\n",
" marked.append(j)\n",
" return marked\n"
],
"metadata": {
"id": "ikf5pcUtRYvV"
Expand Down Expand Up @@ -222,7 +242,59 @@
{
"cell_type": "code",
"source": [
"#Votre code ici"
"import numpy as np\n",
"state_map = {'M': 0, 'D': 1, 'I': 2}\n",
"def build_HMM(A, mark):\n",
" N = len(mark)\n",
" T = np.ones((N+1, 9))\n",
" e_M = np.ones((N+1, 20))\n",
" e_I = np.ones((N+1, 20))\n",
" e_M[0, :] = 0\n",
"\n",
" for k in range(len(A)):\n",
" pi = []\n",
"\n",
" for l in range(len(A[k])):\n",
" if l in mark:\n",
" pi.append('D' if A[k][l] == '-' else 'M')\n",
" else:\n",
" pi.append(None if A[k][l] == '-' else 'I')\n",
"\n",
" l0 = next((l for l in range(len(pi)) if pi[l] is not None), None)\n",
" if l0 is not None:\n",
" if pi[l0] == 'I':\n",
" e_I[0, P[A[k][l0]]] += 1\n",
" T[0, state_map[pi[l0]]] += 1\n",
"\n",
" u = 0\n",
" for l in range(l0, len(A[k])):\n",
" if l in mark:\n",
" u += 1\n",
" if pi[l] is None:\n",
" continue\n",
" if pi[l] == 'M' and A[k][l] != '-':\n",
" e_M[u, P[A[k][l]]] += 1\n",
" elif pi[l] == 'I' and A[k][l] != '-':\n",
" e_I[u, P[A[k][l]]] += 1\n",
"\n",
" v = next((v for v in range(l+1, len(A[k])) if pi[v] is not None), None)\n",
" idx = state_map[pi[l]] * 3 + state_map[pi[v]] if v is not None else state_map[pi[l]] * 3\n",
" T[u, idx] += 1\n",
"\n",
" for i in range(T.shape[0]):\n",
" row_sum = np.sum(T[i, :])\n",
" if row_sum > 0:\n",
" T[i, :] /= row_sum\n",
"\n",
" e_M /= e_M.sum(axis=1, keepdims=True)\n",
" e_I /= e_I.sum(axis=1, keepdims=True)\n",
"\n",
" T = np.round(T, 3)\n",
" e_M= np.round(e_M, 3)\n",
" e_I = np.round(e_I, 3)\n",
"\n",
" return T, e_M, e_I\n",
"\n"
],
"metadata": {
"id": "Y3TXPqNhTwNo"
Expand Down Expand Up @@ -301,7 +373,67 @@
{
"cell_type": "code",
"source": [
"#Votre code ici"
"def viterbi_fwd(T, e_M, e_I, s):\n",
" N = T.shape[0] - 1\n",
" M = len(s)\n",
" V = np.full((3*N+1, M+1), -np.inf)\n",
" B = np.empty((3*N+1, M+1), dtype=object)\n",
" V[0, 0] = 0\n",
" for j in range(1, M+1):\n",
" for i in range(2, 3*N):\n",
" u = i // 3\n",
" state = i % 3\n",
" if state == 0:\n",
" V[i, j] = np.log(e_M[u, P[s[j-1]]]) + max(\n",
" V[i-3, j-1] + np.log(T[u-1, 0]),\n",
" V[i-2, j-1] + np.log(T[u-1, 3]),\n",
" V[i-1, j-1] + np.log(T[u-1, 6])\n",
" )\n",
" if V[i, j] == V[i-3, j-1] + np.log(T[u-1, 0]):\n",
" B[i, j] = (i-3, j-1)\n",
" elif V[i, j] == V[i-2, j-1] + np.log(T[u-1, 3]):\n",
" B[i, j] = (i-2, j-1)\n",
" else:\n",
" B[i, j] = (i-1, j-1)\n",
"\n",
" elif state == 1:\n",
" V[i, j] = max(\n",
" V[i-4, j] + np.log(T[u-1, 1]),\n",
" V[i-3, j] + np.log(T[u-1, 4]),\n",
" V[i-2, j] + np.log(T[u-1, 7])\n",
" )\n",
" if V[i, j] == V[i-4, j] + np.log(T[u-1, 1]):\n",
" B[i, j] = (i-4, j)\n",
" elif V[i, j] == V[i-3, j] + np.log(T[u-1, 4]):\n",
" B[i, j] = (i-3, j)\n",
" else:\n",
" B[i, j] = (i-2, j)\n",
" elif state == 2:\n",
" V[i, j] = np.log(e_I[u, P[s[j-1]]]) + max(\n",
" V[i-2, j-1] + np.log(T[u-1, 2]),\n",
" V[i-1, j-1] + np.log(T[u-1, 5]),\n",
" V[i, j-1] + np.log(T[u, 8])\n",
" )\n",
" if V[i, j] == V[i-2, j-1] + np.log(T[u-1, 2]):\n",
" B[i, j] = (i-2, j-1)\n",
" elif V[i, j] == V[i-1, j-1] + np.log(T[u-1, 5]):\n",
" B[i, j] = (i-1, j-1)\n",
" else:\n",
" B[i, j] = (i, j-1)\n",
" for j in range(M+1):\n",
" V[3*N, j] = max(\n",
" V[3*N-3, j] + np.log(T[N-1, 0]),\n",
" V[3*N-2, j] + np.log(T[N-1, 3]),\n",
" V[3*N-1, j] + np.log(T[N-1, 6])\n",
" )\n",
" if V[3*N, j] == V[3*N-3, j] + np.log(T[N-1, 0]):\n",
" B[3*N, j] = (3*N-3, j)\n",
" elif V[3*N, j] == V[3*N-2, j] + np.log(T[N-1, 3]):\n",
" B[3*N, j] = (3*N-2, j)\n",
" else:\n",
" B[3*N, j] = (3*N-1, j)\n",
" return V, B\n",
"\n"
],
"metadata": {
"id": "2AxydaWBbPe9"
Expand Down Expand Up @@ -335,13 +467,117 @@
{
"cell_type": "code",
"source": [
"#Votre code ici"
"\n",
"def viterbi_bwd(V, B, s):\n",
" N = (V.shape[0] - 1) // 3\n",
" M = len(s)\n",
" i, j = 3*N, M\n",
"\n",
" pi = []\n",
" aligned_s = []\n",
"\n",
" while j > 0 and i > 0:\n",
" prev_i, prev_j = B[i, j] if B[i, j] is not None else (0, 0)\n",
"\n",
" if i % 3 == 0:\n",
" aligned_s.append(s[j-1])\n",
" pi.append('M')\n",
" elif i % 3 == 1:\n",
" aligned_s.append('-')\n",
" pi.append('D')\n",
" else:\n",
" aligned_s.append(s[j-1])\n",
" pi.append('I')\n",
"\n",
" i, j = prev_i, prev_j\n",
"\n",
" return V[3*N, M], ''.join(reversed(pi)), ''.join(reversed(aligned_s))\n",
"\n"
],
"metadata": {
"id": "48vtEZxoAkeE"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"source": [
"seq = read_fasta(\"easy1.fasta\")\n",
"mark = mark_columns(seq, 0.3)\n",
"T, e_M, e_I = build_HMM(seq, mark)\n",
"\n",
"print(T)\n",
"print(\"\\n\")\n",
"print(e_M)\n",
"print(\"\\n\")\n",
"print(e_I)\n",
"print(\"\\n\")\n",
"\n",
"s_easy1_seq1 = 'RAPWEDYNMT'\n",
"T = np.array(T)\n",
"V, B = viterbi_fwd(T, e_M, e_I, s_easy1_seq1)\n",
"score, pi, aligned_s = viterbi_bwd(V, B, s_easy1_seq1)\n",
"\n",
"print(score)\n",
"print(\"\\n\")\n",
"\n",
"print(aligned_s)\n",
"print(pi)\n",
"print(\"\\n\")\n"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "2QCF0LjEAgnC",
"outputId": "8276ed05-8632-4517-ae37-0c36f0e38672"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"[[0.357 0.143 0.071 0.071 0.071 0.071 0.071 0.071 0.071]\n",
" [0.042 0.042 0.208 0.042 0.042 0.083 0.208 0.083 0.25 ]\n",
" [0.357 0.071 0.071 0.143 0.071 0.071 0.071 0.071 0.071]]\n",
"\n",
"\n",
"[[ nan nan nan nan nan nan nan nan nan nan nan nan\n",
" nan nan nan nan nan nan nan nan]\n",
" [0.042 0.042 0.042 0.208 0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042\n",
" 0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042]\n",
" [0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042 0.042\n",
" 0.042 0.042 0.042 0.042 0.042 0.042 0.208 0.042]]\n",
"\n",
"\n",
"[[0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05\n",
" 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 ]\n",
" [0.033 0.033 0.033 0.233 0.033 0.033 0.033 0.033 0.033 0.167 0.033 0.033\n",
" 0.033 0.033 0.033 0.033 0.033 0.033 0.033 0.033]\n",
" [0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05\n",
" 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 ]]\n",
"\n",
"\n",
"-48.252451213623715\n",
"\n",
"\n",
"RAPWEDYNMTT\n",
"IIIIIIIIIIM\n",
"\n",
"\n"
]
},
{
"output_type": "stream",
"name": "stderr",
"text": [
"<ipython-input-8-0895446c9b5e>:45: RuntimeWarning: invalid value encountered in divide\n",
" e_M /= e_M.sum(axis=1, keepdims=True)\n"
]
}
]
}
]
}