docs/notebooks/CRISPR.ipynb

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    "# How to Model CRISPR-Cas9 Experiments in pydna\n",
    "\n",
    "> Visit the full library documentation [here](https://bjornfjohansson.github.io/pydna/)\n",
    "\n",
    "The pydna package can simulate CRISPR-Cas9 editing, which allows one to cut DNA sequences at specific sites using guide RNAs (gRNAs) that direct the Cas9 protein. This page will guide you through the process of using the `pydna.crispr` module to model a CRISPR-Cas9 cut on a DNA sequence.\n",
    "\n",
    "The `pydna.crispr` module contains the `cas9` class to simulate the biological activites of the Cas9 protein and the guideRNA, which should be imported. In addtion, the `Dseqrecord` class has also been imported to generate an example target_sequence."
   ]
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    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/BjornFJohansson/pydna/blob/dev_bjorn/docs/notebooks/CRISPR.ipynb\">\n",
    "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
    "</a>"
   ]
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  {
   "cell_type": "code",
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   "source": [
    "# Install pydna (only when running on Colab)\n",
    "import sys\n",
    "if 'google.colab' in sys.modules:\n",
    "    %%capture\n",
    "    # Install the current development version of pydna (comment to install pip version)\n",
    "    !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
    "    # Install pip version instead (uncomment to install)\n",
    "    # !pip install pydna\n"
   ]
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  {
   "cell_type": "code",
   "execution_count": null,
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   "source": [
    "from pydna.crispr import cas9, protospacer\n",
    "from pydna.dseqrecord import Dseqrecord"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The target sequence and guideRNA (gRNA) sequence needs to be generated. Note the the sequence can be passed as a `Dseqrecord` object."
   ]
  },
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     "text": [
      "cutting with enzyme 1: (Dseqrecord(-17), Dseqrecord(-6))\n",
      "protospacer: GTTACTTTACCCGACGTCCC\n",
      "cutting with enzyme 2: (Dseqrecord(-17), Dseqrecord(-6))\n",
      "cutting with no PAM in target: ()\n"
     ]
    }
   ],
   "source": [
    "from pydna.dseqrecord import Dseqrecord\n",
    "from pydna.crispr import cas9, protospacer\n",
    "\n",
    "#         <----protospacer---><-------scaffold----------------->\n",
    "guide =  \"GTTACTTTACCCGACGTCCCgttttagagctagaaatagcaagttaaaataagg\"\n",
    "target = \"GTTACTTTACCCGACGTCCCaGG\"\n",
    "#                             <->\n",
    "#                             PAM\n",
    "\n",
    "# Create an enzyme object with the protospacer\n",
    "enzyme = cas9(\"GTTACTTTACCCGACGTCCC\")\n",
    "\n",
    "target_dseq = Dseqrecord(target)\n",
    "\n",
    "# Cut using the enzyme\n",
    "print('cutting with enzyme 1:', target_dseq.cut(enzyme))\n",
    "\n",
    "\n",
    "# Get the protospacer from the full gRNA sequence\n",
    "gRNA_protospacers = protospacer(Dseqrecord(guide), cas=cas9)\n",
    "# Print the protospacer (it's a list because often plasmids contain multiple gRNAs)\n",
    "print('protospacer:', gRNA_protospacers[0])\n",
    "gRNA_protospacer = gRNA_protospacers[0]\n",
    "\n",
    "# Create an enzyme from the protospacer\n",
    "enzyme2 = cas9(gRNA_protospacer)\n",
    "\n",
    "# Simulate the cut\n",
    "print('cutting with enzyme 2:', target_dseq.cut(enzyme2))\n",
    "\n",
    "\n",
    "# Note that without the PAM, the cut will not be made.\n",
    "\n",
    "target_noPAM_dseq = Dseqrecord(\"GTTACTTTACCCGACGTCCCaaa\")\n",
    "print(\"cutting with no PAM in target:\", target_noPAM_dseq.cut(enzyme2))"
   ]
  }
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