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rendu LAURANE DECKERS #1

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68 changes: 58 additions & 10 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 @@ -60,7 +57,7 @@
"metadata": {
"id": "A8LhiAAeP9u-"
},
"execution_count": null,
"execution_count": 1,
"outputs": []
},
{
Expand All @@ -75,6 +72,8 @@
{
"cell_type": "code",
"source": [
"import numpy as np\n",
"\n",
"def read_fasta(fname):\n",
" #Read a fasta file with multiple entries.\n",
" #Returns a list of sequences.\n",
Expand Down Expand Up @@ -123,7 +122,7 @@
"metadata": {
"id": "30qlDWTmQ47E"
},
"execution_count": null,
"execution_count": 3,
"outputs": []
},
{
Expand Down Expand Up @@ -184,12 +183,20 @@
{
"cell_type": "code",
"source": [
"#Votre code ici"
"def mark_columns(A: list, alpha: float) -> list :\n",
" marked = []\n",
" for i in range(len(A)) :\n",
" count = 0\n",
" for char in len(A[i]) :\n",
" count += char == \"-\"\n",
" if count / len(A[i]) < alpha :\n",
" marked.append(i)\n",
" return marked"
],
"metadata": {
"id": "ikf5pcUtRYvV"
},
"execution_count": null,
"execution_count": 4,
"outputs": []
},
{
Expand Down Expand Up @@ -222,7 +229,48 @@
{
"cell_type": "code",
"source": [
"#Votre code ici"
"def build_HMM(A: list, mark: list) :\n",
" # Step 1: init matrixes\n",
" N = len(mark)\n",
" T = np.ones(shape=(N+1, 9))\n",
" eM = np.ones(shape=(N+1, 20))\n",
" eI = np.ones(shape=(N+1, 20))\n",
" T[:,0] = 0\n",
" T[:,T.shape[1] - 1] = 0\n",
" eM[:,0] = 0\n",
"\n",
" # Step 2: fill matrixes\n",
" pi = []\n",
" for k in range(1, len(A)) :\n",
" for l in range(1, len(A[k])):\n",
" if l in mark :\n",
" if A[k][l] == \"-\" :\n",
" pi[l] = \"D\"\n",
" else :\n",
" pi[l] = \"M\"\n",
" else :\n",
" if A[k][l] == \"-\" :\n",
" pi[l] = \"0\"\n",
" else :\n",
" pi[l] = \"I\"\n",
"\n",
" l0 = 0\n",
" while l0 < len(pi) and A[k][l0] == \"-\" :\n",
" l0 += 1\n",
" if l0 == len(pi) :\n",
" eI[0][A[k][l0]]\n",
" T[0][M] += A[k][l0]\n",
"\n",
" u = 0\n",
" for l in range(l0, len(pi)) :\n",
" if l in mark :\n",
" u += 1\n",
" elif pi[l] == \"0\" :\n",
" continue\n",
" elif pi[l] == \"M\" and A[k][l] != \"-\" :\n",
" eM[u][A[k][l]] += 1\n",
" elif pi[l] == \"I\" and A[k][l] != \"-\" :\n",
" eI[u][A[k][l]] += 1"
],
"metadata": {
"id": "Y3TXPqNhTwNo"
Expand Down