{
 "metadata": {
  "name": "",
  "signature": "sha256:7fae145c4fc09c2f52c40801ba213b4320595c585d5a20676c17c7723d8420da"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "record = SeqIO.read(\"sequence.gb\", \"genbank\")\n",
      "\n",
      "info=[]\n",
      "icds=[]\n",
      "seqcds=[]\n",
      "\n",
      "info.append(record.features)\n",
      "\n",
      "for i in xrange(len(record.features)):\n",
      "    if record.features[i].type == \"CDS\":\n",
      "        icds.append(i)\n",
      "for k in icds:\n",
      "   seqcds.append(record.features[k].qualifiers['translation'][0])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "C\u00f3digo da parte II em que s\u00e3o guardadas todas as sequ\u00eancias das features do tipo CDS numa matriz"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "save_file = open(\"my_blast.xml\", \"w\")       \n",
      "for cds in seqcds:\n",
      "    result_handle = NCBIWWW.qblast(\"blastp\", \"swissprot\", cds)\n",
      "    save_file.write(result_handle.read())\n",
      "    save_file.write('\\n')\n",
      "save_file.close()\n",
      "result_handle.close()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "Abre o ficheiro my_blast.xml com permiss\u00e3o para escrita. O ciclo for far\u00e1 a blast para cada sequ\u00eancia CDS guardadas anteriormente. Foi usada a base de dados swissprot, ap\u00f3s o blast o resultado \u00e9 escrito no ficheiro xml e de seguida \u00e9 adicionado uma linha para separar o resultado seguinte."
     ]
    }
   ],
   "metadata": {}
  }
 ]
}