Used for gregcaporaso/An-Introduction-to-Applied-Bioinformatics#140 to convert the ipython notebooks to markdown files.

iab-ipynb-to-md.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Hello world!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "***WROTE: book/Index.md\n",
      "***WROTE: book/applications/biological-diversity.md\n",
      "***WROTE: book/fundamentals/database-searching.md\n",
      "***WROTE: book/fundamentals/msa-assignment.md\n",
      "***WROTE: book/fundamentals/multiple-sequence-alignment.md\n",
      "***WROTE: book/fundamentals/pairwise-alignment-exercises.md\n",
      "***WROTE: book/fundamentals/pairwise-alignment.md\n",
      "***WROTE: book/fundamentals/phylogeny-reconstruction.md\n",
      "***WROTE: book/fundamentals/sequence-mapping-and-clustering.md\n",
      "***WROTE: book/getting-started/reading-iab.md\n"
     ]
    }
   ],
   "source": [
    "from random import random\n",
    "import hashlib\n",
    "\n",
    "def randhash():\n",
    "    m = hashlib.sha1()\n",
    "    m.update(str(random()))\n",
    "    return m.hexdigest()[:6]\n",
    "\n",
    "import os\n",
    "ind = '/Users/caporaso/temp/An-Introduction-To-Applied-Bioinformatics-master/'\n",
    "d = 'book'\n",
    "try:\n",
    "    os.makedirs('./%s' % d)\n",
    "except OSError:\n",
    "    pass\n",
    "\n",
    "cmd = \"ipython nbconvert %s --to markdown --output %s\"\n",
    "\n",
    "for root, dirs, files in os.walk(ind):\n",
    "    out_root = root.replace(ind, \"\")\n",
    "    for f in files:\n",
    "        if '.ipynb_checkpoints' in root: continue\n",
    "        fn, ext = os.path.splitext(f)\n",
    "        if ext =='.ipynb':\n",
    "            try:\n",
    "                os.makedirs(os.path.join(d, out_root))\n",
    "            except OSError:\n",
    "                pass\n",
    "            inf = os.path.join(root, f)\n",
    "            outf = os.path.join(d, out_root, '%s.md' % fn)\n",
    "            x = cmd % (inf, outf)\n",
    "            y = !$x\n",
    "            lines = open(outf)\n",
    "            out_lines = []\n",
    "            in_code = False\n",
    "            for line in lines:\n",
    "                line = line.strip('\\n')\n",
    "                if line.startswith('    '):\n",
    "                    if not in_code:\n",
    "                        in_code = True\n",
    "                        out_lines.append('```python')\n",
    "                    line = line[4:]\n",
    "                    if len(line) > 0:\n",
    "                        out_lines.append('>>> %s' % line)\n",
    "                    else:\n",
    "                        out_lines.append('...')\n",
    "                else:\n",
    "                    if in_code:\n",
    "                        in_code = False\n",
    "                        out_lines.append('```')\n",
    "                    \n",
    "                    if line.startswith('#'):\n",
    "                        out_lines.append(\"%s <link src='%s'/> \"% (line, randhash()))\n",
    "                    else:\n",
    "                        out_lines.append(line)\n",
    "            if in_code:\n",
    "                out_lines.append('```')\n",
    "            outs = '\\n'.join(out_lines)\n",
    "            outs = outs.replace('\\n\\n\\n', '\\n\\n')\n",
    "            open(outf, 'w').write(outs)\n",
    "            print \"***WROTE: %s\" % outf"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'021fa4'"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}