gistfile1.txt

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  {
   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "This dictionary has all the 14 serotypes of salmonella in it. It has the different ebgs associated with each one and the different sts in each ebgs."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sero_ebg_st = {'typhimurium':{1:{'19':140, '34':184, '35':0, '98':0, '99':0, '128':1, '137':0, '159':0, '204':0, '205':0, '209':0, '213':1, '302':0, '313':7, '323':2, '328':0, '332':0, '376':0, '394':0, '429':0, '456':0}, 26:{'15':0}, 54:{'13':0}, 138:{'36':11, 'SLV36':5}}, 'enteritidis':{4:{'11':329, '11SLV':7, '136':0, '168':0, '183':11, '310':0, '366':0, '460':0, '616':0, '640':0, '691':0, '745':0, '814':1, '1479':0}, 93:{'172':0, '180':0}, 32:{'74':1}}, 'agona':{54:{'13':29, '37':0, '1215':0, '1328':0}, 26:{'15':0}, 83:{'463':0}}, 'braenderup':{24:{'22': 5, '21':0, '194':0, '311':8}}, 'infantis':{31:{'32':22, 'SLV32':1, '41':0, '295':0, '1032':0}}, 'parab-java':{19:{'88':4, '127':0, '372':0}, 5:{'43':12, '86':0, '110':0, '149':4, '264':0, '265':0, '266':0, '267':0, '307':1, '325':0, '570':0, '772':0, '896':0}, 32:{'42':2, '423':3, '681':0, '733':0, '734':0}, 155:{'404':0, '679':0}, 59:{'28':2}}, 'kentucky':{164:{'314':3, 'SLV314':1, '832':0}, 56:{'198':10, '727':0}, 15:{'151':0, '152':0, '221':0, '318':0, '723':0}}, 'montevideo':{208:{'749':0, '1491':0}, 39:{'138':4, '748':0, '1518':0}, 4:{'4':3, '81':1, '195':1, '305':0, '316':6, '699':0, '1488':0, '1489':0, '1493':0, '1531':1, '1535':0, '1536':0, '1537':0}}, 'newport':{3:{'45':4, '46':1, '116':0, '121':0, '125':0, '131':0, '157':0, '158':0, '165':0, '184':0, '193':0, '201':0, '211':0, '350':0, '353':0, '355':0, '614':1, '1496':0}, 2:{'5':0, '115':0, '117':0, '118':7, 'SLV118':1, '119':0, '120':0, '122':0, '123':0, '163':0, '164':1, '167':1, '187':0, '189':0, '190':0, '199':0, '223':0, '345':0, '347':0, '351':0, '352':0, '354':0, '375':0}, 35:{'156':1, '166':2, '360':0}, 7:{'31':2, '132':0, '188':0, '191':0, '200':0, '346':0, '348':0, '349':0}, 154:{'807':0, '808':0}}, 'oranienburg':{203:{'1392':0, '1512':0, '1513':0, '1538':0}, 44:{'169':0, '174':4, '320':0, '1515':0, '1516':0, '1553':0}, 45:{'292':0}, 50:{'91':0, '1514':0}, 52:{'179':0}, 41:{'23':0, '47':0, '1522':0, '1523':0}}, 'paratyphi-a':{11:{'495':0, '85':19, 'SLV85':1, '479':0, '494':0, '129':10, '130':1}}, 'stanley':{29:{'29':12, 'DLV29':1, '51':0, 'SLV51':2, '182':0, '1027':0}}, 'typhi':{13:{'1':20, '2':10, 'SLV2':1, '3':0, '8':0, '890':0, '892':0, '911':0}}, 'virchow':{9:{'16':16, 'SLV16':1, 'TLV16':1, '38':0, '181':6, '303':0, '326':0, '359':2, '618':0, '648':1, '755':1}, 70:{'197':6, '333':0}}}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "The below code will tell you how many E-burst groups there are in each serotype"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for serotype in sero_ebg_st:\n",
      "    print serotype, '\\t', len(sero_ebg_st[serotype])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "parab-java \t5\n",
        "enteritidis \t3\n",
        "typhimurium \t4\n",
        "braenderup \t1\n",
        "infantis \t1\n",
        "stanley \t1\n",
        "oranienburg \t6\n",
        "virchow \t2\n",
        "kentucky \t3\n",
        "agona \t3\n",
        "typhi \t1\n",
        "newport \t5\n",
        "paratyphi-a \t1\n",
        "montevideo \t3\n"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "The below code will tell you the names of the EBGs associated with  how many STs there are in each"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "serotype_of_interest = 'typhimurium'\n",
      "\n",
      "for ebg in sero_ebg_st[serotype_of_interest]:\n",
      "    print ebg, '\\t', len(sero_ebg_st[serotype_of_interest][ebg])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "1 \t21\n",
        "26 \t1\n",
        "138 \t2\n",
        "54 \t1\n"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}