{
 "metadata": {
  "name": "",
  "signature": "sha256:a1701052658b9f076fefcac9f1376b132e9acceb3d7ae6052701b6ddb797d178"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Parte II"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from Bio import SeqIO\n",
      "record = SeqIO.read(\"sequence.gb\", \"genbank\")\n",
      "info=[]\n",
      "info.append(record.features)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "L\u00ea o ficheiro do genbank e guarda as features de modo a permitir analisar as informa\u00e7\u00f5es."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "icds=[]\n",
      "seqcds=[]\n",
      "annotations=[],[]\n",
      "\n",
      "for i in xrange(len(record.features)):\n",
      "    if record.features[i].type == \"CDS\":\n",
      "        icds.append(i)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "Guarda as features do tipo CDS"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for k in icds:\n",
      "   seqcds.append(record.features[k].qualifiers['translation'][0])\n",
      "   annotations[0].append(record.features[k].qualifiers['protein_id'])\n",
      "   if 'function' in record.features[k].qualifiers:\n",
      "       annotations[1].append(record.features[k].qualifiers['function'])\n",
      "   else:\n",
      "       annotations[1].append('-')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Para cada feature CDS guardada anteriormente ir\u00e1 guardar no annotations o id da sequ\u00eancia proteica e ainda a fun\u00e7\u00e3o se esta existir, caso n\u00e3o exista colocar\u00e1 um '-'."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "   if record.features[k].qualifiers['product']==['hypothetical protein']:\n",
      "      hipotetica+=1  "
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "Conta o n\u00famero de proteinas hipot\u00e9ticas."
     ]
    }
   ],
   "metadata": {}
  }
 ]
}