Mineração dos promotores de Vigna.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Vigun01g000100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Vigun01g000200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Vigun01g000300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Vigun01g000400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Vigun01g000500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Vigun01g000600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Vigun01g000700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Vigun01g000800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Vigun01g000900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Vigun01g001000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Vigun01g001100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Vigun01g001200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Vigun01g001300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Vigun01g001400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Vigun01g001500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Vigun01g001600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Vigun01g001700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Vigun01g001800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Vigun01g001900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Vigun01g002000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Vigun01g002100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Vigun01g002200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Vigun01g002300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>Vigun01g002400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>Vigun01g002500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Vigun01g002600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>Vigun01g002700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Vigun01g002800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>Vigun01g002900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>Vigun01g003000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29743</th>\n",
       "      <td>VigunL086300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29744</th>\n",
       "      <td>VigunL086400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29745</th>\n",
       "      <td>VigunL086500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29746</th>\n",
       "      <td>VigunL086600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29747</th>\n",
       "      <td>VigunL086700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29748</th>\n",
       "      <td>VigunL086800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29749</th>\n",
       "      <td>VigunL086900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29750</th>\n",
       "      <td>VigunL087000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29751</th>\n",
       "      <td>VigunL087100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29752</th>\n",
       "      <td>VigunL087200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29753</th>\n",
       "      <td>VigunL087300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29754</th>\n",
       "      <td>VigunL087400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29755</th>\n",
       "      <td>VigunL087500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29756</th>\n",
       "      <td>VigunL087600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29757</th>\n",
       "      <td>VigunL087700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29758</th>\n",
       "      <td>VigunL087800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29759</th>\n",
       "      <td>VigunL087900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29760</th>\n",
       "      <td>VigunL088000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29761</th>\n",
       "      <td>VigunL088100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29762</th>\n",
       "      <td>VigunL088200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29763</th>\n",
       "      <td>VigunL088300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29764</th>\n",
       "      <td>VigunL088400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29765</th>\n",
       "      <td>VigunL088500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29766</th>\n",
       "      <td>VigunL088600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29767</th>\n",
       "      <td>VigunL088700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29768</th>\n",
       "      <td>VigunL088800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29769</th>\n",
       "      <td>VigunL088900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29770</th>\n",
       "      <td>VigunL089000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29771</th>\n",
       "      <td>VigunL089100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29772</th>\n",
       "      <td>VigunL089200</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>29773 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   id\n",
       "0      Vigun01g000100\n",
       "1      Vigun01g000200\n",
       "2      Vigun01g000300\n",
       "3      Vigun01g000400\n",
       "4      Vigun01g000500\n",
       "5      Vigun01g000600\n",
       "6      Vigun01g000700\n",
       "7      Vigun01g000800\n",
       "8      Vigun01g000900\n",
       "9      Vigun01g001000\n",
       "10     Vigun01g001100\n",
       "11     Vigun01g001200\n",
       "12     Vigun01g001300\n",
       "13     Vigun01g001400\n",
       "14     Vigun01g001500\n",
       "15     Vigun01g001600\n",
       "16     Vigun01g001700\n",
       "17     Vigun01g001800\n",
       "18     Vigun01g001900\n",
       "19     Vigun01g002000\n",
       "20     Vigun01g002100\n",
       "21     Vigun01g002200\n",
       "22     Vigun01g002300\n",
       "23     Vigun01g002400\n",
       "24     Vigun01g002500\n",
       "25     Vigun01g002600\n",
       "26     Vigun01g002700\n",
       "27     Vigun01g002800\n",
       "28     Vigun01g002900\n",
       "29     Vigun01g003000\n",
       "...               ...\n",
       "29743    VigunL086300\n",
       "29744    VigunL086400\n",
       "29745    VigunL086500\n",
       "29746    VigunL086600\n",
       "29747    VigunL086700\n",
       "29748    VigunL086800\n",
       "29749    VigunL086900\n",
       "29750    VigunL087000\n",
       "29751    VigunL087100\n",
       "29752    VigunL087200\n",
       "29753    VigunL087300\n",
       "29754    VigunL087400\n",
       "29755    VigunL087500\n",
       "29756    VigunL087600\n",
       "29757    VigunL087700\n",
       "29758    VigunL087800\n",
       "29759    VigunL087900\n",
       "29760    VigunL088000\n",
       "29761    VigunL088100\n",
       "29762    VigunL088200\n",
       "29763    VigunL088300\n",
       "29764    VigunL088400\n",
       "29765    VigunL088500\n",
       "29766    VigunL088600\n",
       "29767    VigunL088700\n",
       "29768    VigunL088800\n",
       "29769    VigunL088900\n",
       "29770    VigunL089000\n",
       "29771    VigunL089100\n",
       "29772    VigunL089200\n",
       "\n",
       "[29773 rows x 1 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Coleta todos os IDs do loci de vigna\n",
    "df = pd.read_csv(\n",
    "    'Loci de Vigna.txt',\n",
    "    sep=',', header=None, names=['id'])\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Coleta 2000 pares de base do promotor para cada gene do genoma de vigna\n",
    "from intermine.webservice import Service\n",
    "service = Service(\"https://phytozome.jgi.doe.gov/phytomine/service\")\n",
    "\n",
    "query = service.new_query(\"Gene\")\n",
    "\n",
    "query.add_view(\n",
    "    \"name\", \"primaryIdentifier\", \"secondaryIdentifier\", \"length\",\n",
    "    \"flankingRegions.length\", \"flankingRegions.includeGene\",\n",
    "    \"flankingRegions.direction\", \"flankingRegions.primaryIdentifier\",\n",
    "    \"flankingRegions.sequence.length\", \"flankingRegions.sequence.residues\"\n",
    ")\n",
    "\n",
    "query.add_constraint(\"flankingRegions.length\", \"=\", \"5000\", code = \"A\")\n",
    "query.add_constraint(\"flankingRegions.includeGene\", \"=\", \"false\", code = \"B\")\n",
    "query.add_constraint(\"flankingRegions.direction\", \"=\", \"upstream\", code = \"C\")\n",
    "query.add_constraint(\"name\", \"CONTAINS\", \"Vigun\", code = \"D\")\n",
    "\n",
    "with open (\"promotores de vigna.txt\", \"w\") as promotores:\n",
    "    for row in query.rows():\n",
    "        promotores.write(str(row[\"primaryIdentifier\"])+' '+\\\n",
    "                         str(row[\"flankingRegions.length\"])+' '+\\\n",
    "                         str(row[\"flankingRegions.direction\"])+' '+\\\n",
    "                         str(row[\"flankingRegions.sequence.residues\"][3000:])+'\\n')"
   ]
  }
 ],
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