1.01_StringBasics.ipynb

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   "source": [
    "# define a new sequence\n",
    "seq = 'ACGT'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
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    "collapsed": true
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   "source": [
    "# define a new sequence\n",
    "seq = \"ACGT\""
   ]
  },
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   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
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   "outputs": [
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     "data": {
      "text/plain": [
       "'C'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
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   ],
   "source": [
    "# Get a character from a string\n",
    "seq[1]"
   ]
  },
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   "execution_count": 4,
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       "4"
      ]
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     "execution_count": 4,
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   ],
   "source": [
    "# get the length of a sequence\n",
    "len(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
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   "outputs": [],
   "source": [
    "# empty string (epsilon)\n",
    "e = ''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
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       "0"
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    "len(e)"
   ]
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   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AACCGGTT\n"
     ]
    }
   ],
   "source": [
    "# concatenation\n",
    "seq1 = 'AACC'\n",
    "seq2 = 'GGTT'\n",
    "print(seq1 + seq2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ACGT\n"
     ]
    }
   ],
   "source": [
    "seqs = ['A', 'C', 'G', 'T']\n",
    "print(''.join(seqs))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'T'"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# generate a random nucleotide\n",
    "import random\n",
    "random.seed(0)\n",
    "random.choice('ACGT')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GTGCACGTTC\n"
     ]
    }
   ],
   "source": [
    "# generate a random sequence\n",
    "seq = ''\n",
    "for _ in range(10): #no need to specify index so can use _\n",
    "    seq += random.choice('ACGT')\n",
    "print(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TCTGAGCTGA\n"
     ]
    }
   ],
   "source": [
    "# another way to generate a random sequence\n",
    "seq = ''.join([random.choice('ACGT') for _ in range(10)])\n",
    "print(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CT'"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# get a substring\n",
    "seq[1:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'TCT'"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# get a prefix\n",
    "seq[:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'TGA'"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# get a suffix\n",
    "seq[7:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'TGA'"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# another way to get a suffix\n",
    "seq[-3:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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