Activity 2

activity_2

{
 "metadata": {
  "name": "statement_2"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Activity 2"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "The file `data/names.txt` has a million lines, each of which contains a saccharomyces cerevisiae gene name."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!wc -l data/names.txt",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "1000000 data/names.txt\r\n"
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!head data/names.txt",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "YIL054W\r\nYOR366W\r\nYNL244C\r\nYNL085W\r\nYDL244W\r\nYGL204C\r\nYNL046W\r\nYIL006W\r\nYBR077C\r\nYHL029C\r\n"
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "Main goal"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "Create a dictionary of (gene name: number of times that gene name appears in the file) pairs."
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "Stretch goals"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "Which gene appears the most?\n\nVisualize the distribution of counts for all names."
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "Super strech goal"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "Implement the naive array-based scheme described in the lecture and compare its speed to using a dictionary."
    }
   ],
   "metadata": {}
  }
 ]
}