Mineração dos promotores de fenilpropanoides.ipynb

{
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  {
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   "source": [
    "import numpy as np\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "                id\n",
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     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_csv(\n",
    "    'loci de fenilpropanoides.txt',\n",
    "    sep=',', header=None, names=['id'])\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "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",
    "\n",
    "with open (\"promotores de fenilpropanoides.txt\", \"w\") as promotores:\n",
    "    for i in df['id']:\n",
    "        query.add_constraint(\"name\", \"=\", i, code = \"D\")\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') #Salvar apenas as ultimas 2000 bases"
   ]
  }
 ],
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