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209 changes: 190 additions & 19 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 +56,54 @@
{
"cell_type": "code",
"source": [
"print(\"votre fonction ici !!\")"
"def BWT(s):\n",
" s += \"$\"\n",
" perm = []\n",
" n = len(s)\n",
" for i in range(n):\n",
" perm.append((s[n-i:] + s[:n-i],i))\n",
" print(perm)\n",
"\n",
" tab = sorted(perm)\n",
" print(tab)\n",
"\n",
" seq = \"\"\n",
" indice = []\n",
" for s,i in tab:\n",
" seq += s[-1]\n",
" indice.append(i)\n",
" return seq, indice\n",
"\n",
"BWT(\"chien\")"
],
"metadata": {
"id": "D5zJsnmQnajj"
"id": "D5zJsnmQnajj",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "24b7c7d1-7eaf-40f1-c519-4ea874549f60"
},
"execution_count": null,
"outputs": []
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"[('chien$', 0), ('$chien', 1), ('n$chie', 2), ('en$chi', 3), ('ien$ch', 4), ('hien$c', 5)]\n",
"[('$chien', 1), ('chien$', 0), ('en$chi', 3), ('hien$c', 5), ('ien$ch', 4), ('n$chie', 2)]\n"
]
},
{
"output_type": "execute_result",
"data": {
"text/plain": [
"('n$iche', [1, 0, 3, 5, 4, 2])"
]
},
"metadata": {},
"execution_count": 23
}
]
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -135,13 +164,155 @@
{
"cell_type": "code",
"source": [
"print(\"Votre code ici !\")"
"def iBWT(t): #Don't work\n",
" tab = []\n",
" n = len(t)\n",
" for i in range(n):\n",
" tmp = []\n",
" for j in range(n):\n",
" word = \"\"\n",
" for k in range(i+1):\n",
" word += t[(k+j)%n]\n",
" tmp.append(word)\n",
" tab.append((tmp, sorted(tmp)))\n",
" return tab\n",
"\n",
"iBWT(\"n$iche\")"
],
"metadata": {
"id": "oH-bAVbgpOUe"
"id": "oH-bAVbgpOUe",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "c1bc8f68-07d6-4ea4-8c29-9353cc937af2"
},
"execution_count": null,
"outputs": []
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"[(['n', '$', 'i', 'c', 'h', 'e'], ['$', 'c', 'e', 'h', 'i', 'n']),\n",
" (['n$', '$i', 'ic', 'ch', 'he', 'en'], ['$i', 'ch', 'en', 'he', 'ic', 'n$']),\n",
" (['n$i', '$ic', 'ich', 'che', 'hen', 'en$'],\n",
" ['$ic', 'che', 'en$', 'hen', 'ich', 'n$i']),\n",
" (['n$ic', '$ich', 'iche', 'chen', 'hen$', 'en$i'],\n",
" ['$ich', 'chen', 'en$i', 'hen$', 'iche', 'n$ic']),\n",
" (['n$ich', '$iche', 'ichen', 'chen$', 'hen$i', 'en$ic'],\n",
" ['$iche', 'chen$', 'en$ic', 'hen$i', 'ichen', 'n$ich']),\n",
" (['n$iche', '$ichen', 'ichen$', 'chen$i', 'hen$ic', 'en$ich'],\n",
" ['$ichen', 'chen$i', 'en$ich', 'hen$ic', 'ichen$', 'n$iche'])]"
]
},
"metadata": {},
"execution_count": 35
}
]
},
{
"cell_type": "code",
"source": [
"def iBWT3(s) -> str:\n",
" inverse = [char for char in s]\n",
" for i in range(len(s) - 1):\n",
" inverse.sort()\n",
" inverse = [s[j] + inverse[j] for j in range(len(s))]\n",
" print(inverse)\n",
" print(inverse)\n",
" return next(elt for elt in inverse if elt[-1] == '$')\n",
"iBWT3(\"n$iche\")"
],
"metadata": {
"id": "BwA537kFnlK3",
"outputId": "358a1db9-b232-4503-9311-f3285f6bc07a",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 142
}
},
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"['n$', '$c', 'ie', 'ch', 'hi', 'en']\n",
"['n$c', '$ch', 'ien', 'chi', 'hie', 'en$']\n",
"['n$ch', '$chi', 'ien$', 'chie', 'hien', 'en$c']\n",
"['n$chi', '$chie', 'ien$c', 'chien', 'hien$', 'en$ch']\n",
"['n$chie', '$chien', 'ien$ch', 'chien$', 'hien$c', 'en$chi']\n",
"['n$chie', '$chien', 'ien$ch', 'chien$', 'hien$c', 'en$chi']\n"
]
},
{
"output_type": "execute_result",
"data": {
"text/plain": [
"'chien$'"
],
"application/vnd.google.colaboratory.intrinsic+json": {
"type": "string"
}
},
"metadata": {},
"execution_count": 1
}
]
},
{
"cell_type": "code",
"source": [
"def iBWT2(t):\n",
" table = [\"\"] * len(t)\n",
"\n",
" for _ in range(len(t)):\n",
" table = [t[i] + table[i] for i in range(len(t))]\n",
" table.sort()\n",
" print(table)\n",
"\n",
" for s in table:\n",
" if s.endswith(\"$\"):\n",
" return s[:-1]\n",
" return \"\"\n",
"\n",
"iBWT2(\"n$iche\")"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 142
},
"id": "tXcgUA4ilNu0",
"outputId": "aeb4b385-0b87-4b76-b6e3-fea867f1b3ff"
},
"execution_count": 2,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"['$', 'c', 'e', 'h', 'i', 'n']\n",
"['$c', 'ch', 'en', 'hi', 'ie', 'n$']\n",
"['$ch', 'chi', 'en$', 'hie', 'ien', 'n$c']\n",
"['$chi', 'chie', 'en$c', 'hien', 'ien$', 'n$ch']\n",
"['$chie', 'chien', 'en$ch', 'hien$', 'ien$c', 'n$chi']\n",
"['$chien', 'chien$', 'en$chi', 'hien$c', 'ien$ch', 'n$chie']\n"
]
},
{
"output_type": "execute_result",
"data": {
"text/plain": [
"'chien'"
],
"application/vnd.google.colaboratory.intrinsic+json": {
"type": "string"
}
},
"metadata": {},
"execution_count": 2
}
]
},
{
"cell_type": "markdown",
Expand Down