tree_convert_mega_to_json.ipynb

{
 "metadata": {
  "name": "parse_mega_to_json.ipynb"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "json_filename = 'x.json'\n",
      "gexf_filename = 'x.gexf'\n",
      "\n",
      "import os\n",
      "#os.chdir(\"C:/Users/David/Documents/Dropbox\")\n",
      "os.chdir(\"C:/_Dropbox/Dropbox\")\n",
      "\n",
      "import pandas as pd\n",
      "df = pd.read_csv(\"gh43treetable.txt\", dtype=str)\n",
      "        "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 26
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "df.columns = [['ancid', 'desc1', 'desc2', 'branchlength1', 'branchlength2']]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 27
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# replace spaces with underscores, then make a list of all ids with duplicates included, then remove duplicates\n",
      "id_list = []\n",
      "for idx, row in df.iterrows():\n",
      "    for field in ['ancid', 'desc1', 'desc2']:\n",
      "        df[field][idx] = (df[field][idx].strip()).replace(\" \", \"_\")\n",
      "        id_list.append(df[field][idx])\n",
      "print len(id_list)\n",
      "id_list = list(set(id_list))\n",
      "print len(id_list)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "639\n",
        "427\n"
       ]
      }
     ],
     "prompt_number": 28
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print df.iloc[2]\n",
      "print id_list[:10]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "ancid                      217\n",
        "desc1                      216\n",
        "desc2             ASPNI_A2QT85\n",
        "branchlength1     0.0000000000\n",
        "branchlength2     0.0000000000\n",
        "Name: 2, dtype: object\n",
        "['Paeby1p7_018872', 'Paeby1p7_018871', 'bri_CHGT_02150', 'ABN43C_PENCH', '344', '345', 'ABN43A_PENCH', 'CORTH_1_02834', '340', '341']\n"
       ]
      }
     ],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# make dicts of IDs and positions in id_list\n",
      "dict_pti = {}\n",
      "dict_itp = {}\n",
      "for pos in range(len(id_list)):\n",
      "    dict_pti[pos] = id_list[pos]\n",
      "    dict_itp[id_list[pos]] = pos"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 31
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#make link list\n",
      "link_list = []\n",
      "for idx, row in df.iterrows():\n",
      "    for descnum in ['desc1', 'desc2']:\n",
      "        templist = []\n",
      "        templist.append(df.ancid[idx])\n",
      "        templist.append(df[descnum][idx])\n",
      "        link_list.append(templist)\n",
      "print link_list[:10]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[['215', 'ABN43A_ASPNG'], ['215', 'ANIG203143G'], ['216', '215'], ['216', 'ASPNI_P42256'], ['217', '216'], ['217', 'ASPNI_A2QT85'], ['218', 'PENCH_Q5H7M8'], ['218', 'ABN43A_PENCH'], ['219', 'Paeby1p7_018872'], ['219', '218']]\n"
       ]
      }
     ],
     "prompt_number": 36
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# write gexf\n",
      "with open(json_filename, \"w\") as f:\n",
      "    f.write('<gexf xmlns=\"http://www.gexf.net/1.2draft\" version=\"1.2\">\\n    <meta lastmodifieddate=\"2009-03-20\">\\n        <creator>Gexf.net</creator>\\n')\n",
      "with open(json_filename, \"a\") as f:\n",
      "    f.write('        <description>')\n",
      "    f.write(\n",
      "    for pos in range(len(id_list)):\n",
      "        f.write('    {\"name\": \"' + dict_pti[pos] + '\"}')\n",
      "        if pos < len(id_list) - 1:\n",
      "            f.write(',\\n')\n",
      "        else:\n",
      "            f.write('\\n')\n",
      "    f.write('  ],\\n  \"links\": [\\n')\n",
      "    for pos in range(len(link_list)):\n",
      "        f.write('    {\"source\": ' + str(dict_itp[link_list[pos][0]]) + ', \"target\": ' + str(dict_itp[link_list[pos][1]]) + '}')\n",
      "        if pos < len(link_list) - 1:\n",
      "            f.write(',\\n')\n",
      "        else:\n",
      "            f.write('\\n')\n",
      "    f.write('  ]\\n}')\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 52
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# write gexf\n",
      "with open(gexf_filename, \"w\") as f:\n",
      "    f.write("
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}