run_crispr_cas9.ipynb

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    "## Instruction for guys from HBV cripr/cas9 research group:\n",
    "\n",
    "1. create a folder named <span style=\"background-color:lightgrey\">input_data</span> in the current directory and paste your files in 'fasta' format into it\n",
    "\n",
    "2. To count indels, click on the cell below which contains the following code:\n",
    "\n",
    "```python\n",
    "%run -m crispr_cas9.count_indels\n",
    "```\n",
    "\n",
    "\n",
    "after that to run the script do one of the following:\n",
    "- click <span style=\"background-color:lightgrey\">Run</span> button on the panel above\n",
    "- or press <span style=\"background-color:lightgrey\">Shift + Enter</span> or <span style=\"background-color:lightgrey\">Ctrl + Enter</span>\n",
    "\n",
    "\n",
    "when the script finishes its work, the results will be written into the folder <span style=\"background-color:lightgrey\">output_indels</span>  in the current directory\n",
    "\n",
    "\n",
    "3. To create matrices, click on the cell below which contains the following code:\n",
    "\n",
    "```python\n",
    "%run -m crispr_cas9.create_matrices\n",
    "```\n",
    "\n",
    "after that to run the script do one of the following:\n",
    "- click <span style=\"background-color:lightgrey\">Run</span> button on the panel above\n",
    "- or press <span style=\"background-color:lightgrey\">Shift + Enter</span> or <span style=\"background-color:lightgrey\">Ctrl + Enter</span>\n",
    "\n",
    "\n",
    "when the script finishes its work, the results will be written into the folder <span style=\"background-color:lightgrey\">output_matrices</span>  in the current directory\n",
    "\n",
    "\n",
    "4. To create plots using the excel spreadsheets made by the previous command, click on the next cell with the code:\n",
    "\n",
    "```python\n",
    "%run -m crispr_cas9.create_plots\n",
    "```\n",
    "and again to run the script do one of the following:\n",
    "- click <span style=\"background-color:lightgrey\">Run</span> button on the panel above\n",
    "- or press <span style=\"background-color:lightgrey\">Shift + Enter</span> or <span style=\"background-color:lightgrey\">Ctrl + Enter</span>\n",
    "\n",
    "when this script finishes its work, the results will be written into the folder <span style=\"background-color:lightgrey\">output_plots</span>  in the current directory\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "NOTES: \n",
    "- if you want to stop running script, click <span style=\"background-color:lightgrey\">stop</span> button on the panel above (which is black square).\n",
    "\n",
    "\n"
   ]
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   "source": [
    "import crispr_cas9"
   ]
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      "\n",
      "    ---------------\n",
      "    job started at 2021-03-23 08:12:04 ...\n",
      "    ---------------\n",
      "    \n"
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      "\n",
      "    \n",
      "    file processed: 2\n",
      "    time taken: 0.0 hours 0.0 minutes 2 seconds\n",
      "    \n",
      "    the results are in the folder 'output_indels'\n",
      "    \n",
      "    ---------------\n",
      "    ... job finished at 2021-03-23 08:12:06\n",
      "    ---------------\n",
      "    \n",
      "    \n"
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   "source": [
    "%run -m crispr_cas9.count_indels"
   ]
  },
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     "text": [
      "\n",
      "    ---------------\n",
      "    job started at 2021-03-23 08:12:15 ...\n",
      "    ---------------\n",
      "    \n"
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      "\n",
      "    \n",
      "    file processed: 2\n",
      "    time taken: 0.0 hours 0.0 minutes 33 seconds\n",
      "    \n",
      "    the results are in the folder 'output_indels'\n",
      "    \n",
      "    ---------------\n",
      "    ... job finished at 2021-03-23 08:12:48\n",
      "    ---------------\n",
      "    \n",
      "    \n"
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   ],
   "source": [
    "%run -m crispr_cas9.create_matrices"
   ]
  },
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     "text": [
      "\n",
      "    ---------------\n",
      "    job started at 2021-03-23 08:12:48 ...\n",
      "    ---------------\n",
      "    \n"
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     "text": [
      "\n",
      "    \n",
      "    file processed: 8\n",
      "    time taken: 0.0 hours 0.0 minutes 29 seconds\n",
      "    \n",
      "    the results are in the folder 'output_plots'\n",
      "    \n",
      "    ---------------\n",
      "    ... job finished at 2021-03-23 08:13:18\n",
      "    ---------------\n",
      "    \n",
      "    \n"
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   ],
   "source": [
    "%run -m crispr_cas9.create_plots"
   ]
  },
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