{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez, Seq, SeqIO\n",
    "from Bio.Alphabet import IUPAC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "Entrez.email = \"put@your_email.here\" \n",
    "hdl = Entrez.efetch(db='nucleotide', id=['NM_002299'], rettype='fasta')  # Lactase gene\n",
    "#for l in hdl:\n",
    "#    print l\n",
    "seq = SeqIO.read(hdl, 'fasta')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "SeqRecord(seq=Seq('ATGGAGCTGTCTTGGCATGTAGTCTTTATTGCCCTGCTAAGTTTTTCATGCTGG...TGA', SingleLetterAlphabet()), id='gi|32481205|ref|NM_002299.2|', name='gi|32481205|ref|NM_002299.2|', description='gi|32481205|ref|NM_002299.2| Homo sapiens lactase (LCT), mRNA', dbxrefs=[])"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "w_seq = seq[11:5795]\n",
    "w_seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "w_hdl = open('example.fasta', 'w')\n",
    "SeqIO.write([w_seq], w_hdl, 'fasta')\n",
    "w_hdl.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'Bio.SeqRecord.SeqRecord'>\n",
      "gi|32481205|ref|NM_002299.2| Homo sapiens lactase (LCT), mRNA\n",
      "ATGGAGCTGT\n",
      "SingleLetterAlphabet()\n"
     ]
    }
   ],
   "source": [
    "recs = SeqIO.parse('example.fasta', 'fasta')\n",
    "for rec in recs:\n",
    "    print(type(rec))\n",
    "    seq = rec.seq\n",
    "    print(rec.description)\n",
    "    print(seq[:10])\n",
    "    print(seq.alphabet)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Seq('ATGGAGCTGTCTTGGCATGTAGTCTTTATTGCCCTGCTAAGTTTTTCATGCTGG...TGA', IUPACUnambiguousDNA())"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "seq = Seq.Seq(str(seq), IUPAC.unambiguous_dna)\n",
    "seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(Seq('ATGGAGCTGTCT', IUPACUnambiguousDNA()), Seq('TCTTCATTCTGA', IUPACUnambiguousDNA()))\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "Seq('AUGGAGCUGUCUUGGCAUGUAGUCUUUAUUGCCCUGCUAAGUUUUUCAUGCUGG...UGA', IUPACUnambiguousRNA())"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print((seq[:12], seq[-12:]))\n",
    "rna = seq.transcribe()\n",
    "rna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Seq('MELSWHVVFIALLSFSCWGSDWESDRNFISTAGPLTNDLLHNLSGLLGDQSSNF...SF*', HasStopCodon(IUPACProtein(), '*'))"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "prot = seq.translate()\n",
    "prot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  }
 ],
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