notebooks/testing-with-nose.ipynb

{
 "metadata": {
  "name": "testing-with-nose"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%file calc_gc.py\n",
      "\n",
      "def calc_gc(dna):\n",
      "    dna = dna.upper()\n",
      "    gc = dna.count('G') + dna.count('C')\n",
      "    at = dna.count('A') + dna.count('T')\n",
      "    \n",
      "    total = gc + at\n",
      "    if total == 0:\n",
      "        return 0.0\n",
      "    \n",
      "    frac = gc / float(total)\n",
      "    return frac\n",
      "\n",
      "def test_correct_counting_gc():\n",
      "    x = calc_gc('ATGC')\n",
      "    assert x == 0.5, x\n",
      "    \n",
      "def test_correct_counting_at():\n",
      "    x = calc_gc('AAAA')\n",
      "    assert x == 0.0, x\n",
      "\n",
      "def test_3():\n",
      "    x = calc_gc('atgc')\n",
      "    assert x == 0.5, x\n",
      "    \n",
      "def test_4():\n",
      "    x = calc_gc('AtgCNN')\n",
      "    assert x == 0.5, x\n",
      "    \n",
      "def test_5():\n",
      "    x = calc_gc('NNNNNN')\n",
      "    assert x == 0.0, x"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Overwriting calc_gc.py"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!nosetests -v calc_gc.py"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "calc_gc.test_correct_counting_gc ... ok\r\n",
        "calc_gc.test_correct_counting_at ... ok\r\n",
        "calc_gc.test_3 ... ok\r\n",
        "calc_gc.test_4 ... ok\r\n",
        "calc_gc.test_5 ... ok\r\n",
        "\r\n",
        "----------------------------------------------------------------------\r\n",
        "Ran 5 tests in 0.001s\r\n",
        "\r\n",
        "OK\r\n"
       ]
      }
     ],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!pip install git+https://github.com/ged-lab/screed.git\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Downloading/unpacking git+https://github.com/ged-lab/screed.git\r\n",
        "  Cloning https://github.com/ged-lab/screed.git to /var/folders/y6/s1r3q87933s6gjdrtmts1npc0000gq/T/pip-Ha7xSv-build\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  Running setup.py egg_info for package from git+https://github.com/ged-lab/screed.git\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "    \r\n",
        "Cleaning up...\r\n"
       ]
      }
     ],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}