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RENDU TANCREDE SALOTTI #15

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267 changes: 234 additions & 33 deletions BINF_TP5.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": "ABX9TyO0SUJI6kaczFcOh8NoKcqb",
"include_colab_link": true
"provenance": []
},
"kernelspec": {
"name": "python3",
Expand All @@ -16,16 +14,6 @@
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/github/pparutto/BINF2025_TP5/blob/main/BINF_TP5.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "markdown",
"source": [
Expand Down Expand Up @@ -68,13 +56,42 @@
{
"cell_type": "code",
"source": [
"print(\"votre fonction ici !!\")"
"def BWT(s):\n",
" s += \"$\"\n",
"\n",
" n = len(s)\n",
" perm = [s[-i:] + s[:-i] for i in range(n)]\n",
"\n",
" indices = list(range(n))\n",
"\n",
" sorted_perm_indices = sorted(zip(perm, indices))\n",
" perm_sorted = [p for p, _ in sorted_perm_indices]\n",
" indices_sorted = [i for _, i in sorted_perm_indices]\n",
"\n",
" last_column = ''.join(p[-1] for p in perm_sorted)\n",
"\n",
" return last_column, indices_sorted\n",
"\n",
"bwt = BWT('chien')\n",
"print(bwt)"
],
"metadata": {
"id": "D5zJsnmQnajj"
"id": "D5zJsnmQnajj",
"outputId": "b72a5830-50a7-4c74-dc8f-f12880823132",
"colab": {
"base_uri": "https://localhost:8080/"
}
},
"execution_count": null,
"outputs": []
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"('n$iche', [1, 0, 3, 5, 4, 2])\n"
]
}
]
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -135,13 +152,39 @@
{
"cell_type": "code",
"source": [
"print(\"Votre code ici !\")"
"def iBWT(t):\n",
" n = len(t)\n",
"\n",
" table = [\"\" for _ in range(n)]\n",
"\n",
" for _ in range(n):\n",
" table = [t[i] + table[i] for i in range(n)]\n",
" table.sort()\n",
"\n",
" for seq in table:\n",
" if seq.endswith(\"$\"):\n",
" return seq[:-1]\n",
"\n",
"ibwt = iBWT(bwt[0])\n",
"print(ibwt)"
],
"metadata": {
"id": "oH-bAVbgpOUe"
"id": "oH-bAVbgpOUe",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "d29a1d77-11b1-4da1-869a-4bcd2d8b1fef"
},
"execution_count": null,
"outputs": []
"execution_count": 2,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"chien\n"
]
}
]
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -185,13 +228,69 @@
{
"cell_type": "code",
"source": [
"print(\"Votre code ici !\")"
"from collections import Counter\n",
"\n",
"def calculate_C(bwt):\n",
" freq = Counter(bwt)\n",
" sorted_chars = sorted(freq)\n",
" C = {}\n",
" total = 0\n",
" for char in sorted_chars:\n",
" C[char] = total\n",
" total += freq[char]\n",
" return C\n",
"\n",
"def calculate_occ(bwt):\n",
" occ = {}\n",
" for char in set(bwt):\n",
" occ[char] = [0] * (len(bwt) + 1)\n",
" for i, char in enumerate(bwt):\n",
" for c in occ:\n",
" occ[c][i + 1] = occ[c][i]\n",
" occ[char][i + 1] += 1\n",
" return occ\n",
"\n",
"def exactmatch(p, bwt):\n",
" C = calculate_C(bwt)\n",
" occ = calculate_occ(bwt)\n",
" p = list(p)\n",
" if p[-1] not in C:\n",
" return -1, -1\n",
" c = p[-1]\n",
" sp = C[c] + 1\n",
" ep = C[c] + occ[c][-1]\n",
" for i in range(len(p) - 2, -1, -1):\n",
" c = p[i]\n",
" if c not in C:\n",
" return -1, -1\n",
" sp = C[c] + occ[c][sp - 1] + 1\n",
" ep = C[c] + occ[c][ep]\n",
" if sp > ep:\n",
" return -1, -1\n",
" return sp, ep\n",
"\n",
"bwt = \"annb$aa\"\n",
"p = \"ana\"\n",
"sp, ep = exactmatch(p, bwt)\n",
"print(f\"Indices sp: {sp}, ep: {ep}\")\n"
],
"metadata": {
"id": "C63yJjfjtUSQ"
"id": "C63yJjfjtUSQ",
"outputId": "819b0940-d7c9-4674-d266-beee0ec002de",
"colab": {
"base_uri": "https://localhost:8080/"
}
},
"execution_count": null,
"outputs": []
"execution_count": 25,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Indices sp: 3, ep: 4\n"
]
}
]
},
{
"cell_type": "markdown",
Expand All @@ -217,13 +316,63 @@
{
"cell_type": "code",
"source": [
"print(\"Votre code ici !\")"
"def stepleft(k, bwt, C, occ):\n",
" char = bwt[k]\n",
" return C[char] + 1 + occ[char][k]\n",
"\n",
"def index_from_match(k, idxs, bwt, C, occ):\n",
" cnt = 0\n",
" while k not in idxs:\n",
" k = stepleft(k, bwt, C, occ)\n",
" cnt += 1\n",
" return (idxs[k] + cnt) % len(bwt)\n",
"\n",
"text = \"chien\"\n",
"bwt_str, idxs, sorted_perms = BWT(text)\n",
"C = calculate_C(bwt_str)\n",
"occ = calculate_occ(bwt_str)\n",
"\n",
"p = \"ien\"\n",
"sp, ep = exactmatch(p, bwt_str)\n",
"\n",
"positions = []\n",
"for k in range(sp - 1, ep):\n",
" pos = index_from_match(k, idxs, bwt_str, C, occ)\n",
" positions.append(pos)\n",
"\n",
"print(positions)\n",
"\n",
"text = \"chien\"\n",
"bwt_str, idxs, sorted_perms = BWT(text)\n",
"\n",
"print(\"Permutations triées :\")\n",
"for i, p in enumerate(sorted_perms):\n",
" print(f\"{i}: {p} (rotation depuis index {idxs[i]})\")"
],
"metadata": {
"id": "3RzUM2FJ91u_"
"id": "3RzUM2FJ91u_",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "53c09e84-6e6f-4e32-a216-76bbd618b57e"
},
"execution_count": null,
"outputs": []
"execution_count": 27,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"[4]\n",
"Permutations triées :\n",
"0: $chien (rotation depuis index 1)\n",
"1: chien$ (rotation depuis index 0)\n",
"2: en$chi (rotation depuis index 3)\n",
"3: hien$c (rotation depuis index 5)\n",
"4: ien$ch (rotation depuis index 4)\n",
"5: n$chie (rotation depuis index 2)\n"
]
}
]
},
{
"cell_type": "markdown",
Expand All @@ -241,13 +390,56 @@
{
"cell_type": "code",
"source": [
"print(\"Votre code ici !\")"
"import random\n",
"\n",
"def BWT_prog(s, k):\n",
" n = len(s)\n",
" seeds = sorted(random.sample(range(1, n), k - 1))\n",
" seeds = [0] + seeds + [n]\n",
"\n",
" print(\"Seeds:\", seeds)\n",
" print(\"Blocks:\", [s[seeds[i]:seeds[i + 1]] for i in range(len(seeds)-1)])\n",
"\n",
" bwt_result = \"\"\n",
" for i in range(len(seeds) - 1):\n",
" block = s[seeds[i]:seeds[i + 1]]\n",
" bwt_result += BWT(block)[0]\n",
"\n",
" return bwt_result\n",
"\n",
"random.seed(42)\n",
"\n",
"text = \"chien\"\n",
"bwt_prog_result_1 = BWT_prog(text, k=1)\n",
"bwt_prog_result = BWT_prog(text, k=3)\n",
"btw = BWT(text)\n",
"print(\"BWT prog result with 1 seed:\", bwt_prog_result_1)\n",
"print(\"BWT full string:\", btw[0])\n",
"print(\"BWT prog result:\", bwt_prog_result)"
],
"metadata": {
"id": "aoWF2thh8zEn"
"id": "aoWF2thh8zEn",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "1d791ee1-d263-40be-8d3c-d744a778d293"
},
"execution_count": null,
"outputs": []
"execution_count": 48,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Seeds: [0, 5]\n",
"Blocks: ['chien']\n",
"Seeds: [0, 1, 4, 5]\n",
"Blocks: ['c', 'hie', 'n']\n",
"BWT prog result with 1 seed: n$iche\n",
"BWT full string: n$iche\n",
"BWT prog result: c$ei$hn$\n"
]
}
]
},
{
"cell_type": "markdown",
Expand All @@ -264,6 +456,15 @@
"metadata": {
"id": "RsY4KN-x83cM"
}
},
{
"cell_type": "code",
"source": [],
"metadata": {
"id": "EEpdjqEGCR6t"
},
"execution_count": null,
"outputs": []
}
]
}