{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "from IPython.display import Image\n",
    "from IPython.display import clear_output\n",
    "from IPython.display import FileLink, FileLinks"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Introduction to\n",
    "\n",
    "![title](img/python-logo-master-flat.png)\n",
    "\n",
    "### with Application to Bioinformatics\n",
    "\n",
    "#### - Day 4"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### TODAY\n",
    "\n",
    "- Loops and functions\n",
    "- Using somebody else's code (using modules)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Review\n",
    "\n",
    "- Why does it matter what type a variable has?\n",
    "- How (and when) can you change the type of those? When does it not work?\n",
    "- You have worked with a number of data containers; lists, sets, dictionaries. What is the difference between them and when should you use which?\n",
    "- What is a function?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Review\n",
    "\n",
    "- Why does it matter what type a variable has?\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "\n",
    "> Values of different types stores different types of information."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "\n",
    "> Different types can be used with different operations, functions and methods."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "1+2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\"1\"+\"2\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\"1\"+2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\"1\"*2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Take extra care when comparing values**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "2<12"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\"2\"<\"12\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Review\n",
    "\n",
    "- How can you change (convert) the type of a value? When does it not work?\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "float(\"1\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "int(\"1\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "str(1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "int(\"2.2\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Converting between strings and lists**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "list(\"hello\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "str(['h', 'e', 'l', 'l', 'o'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "''.join(['h', 'e', 'l', 'l', 'o'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Review\n",
    "\n",
    "\n",
    "- You have worked with a number of data containers; lists, sets, dictionaries. What is the difference between them and when should you use which?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    " - lists: when order is important\n",
    " - dictionaries: to keep track of the relation between keys and values\n",
    " - sets: to check for membership. No order, no duplicates."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mylist = [\"comedy\", \"drama\", \"drama\", \"sci-fi\"]\n",
    "mydict = {\"genre\": \"drama\", \"title\": \"Toy Story\"}\n",
    "myset = set(mylist)\n",
    "print('All genres', myset)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Review\n",
    "\n",
    "- What is a function?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "> A named piece of code that performs a specific task.\n",
    "\n",
    "> A relation between input data (parameters) and a result (output data)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Function structure\n",
    "\n",
    "<img src=\"img/function_structure_explained.png\" alt=\"Drawing\" style=\"width: 600px;\"/>  "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- The `def` keyword"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Arguments"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Indentation!\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- `return`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Scope**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "a"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "def myfunc(a, b):\n",
    "    print(a)\n",
    "    \n",
    "a"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "a = 5\n",
    "\n",
    "def myfunc(a):\n",
    "    a += 2\n",
    "    return a\n",
    "    \n",
    "b = myfunc(8)\n",
    "\n",
    "a, b"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "a = 3\n",
    "print('Globally, a is', a)\n",
    "\n",
    "def myfunc(a):\n",
    "    print('In f, a is', a)\n",
    "    a += 2\n",
    "    print('Then a in f is', a)\n",
    "    return a\n",
    "    \n",
    "print('Calling f with argument 8')\n",
    "b = myfunc(8)\n",
    "print('Result of f(8) =', b)\n",
    "print('Finally the global a is', a)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "The local `a` in `myfunc` *shadows* the global `a`."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "The variables inside functions are *local*. To avoid confusion, use different variable names."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "global_a = 3\n",
    "\n",
    "def myfunc(value):\n",
    "    value += 2\n",
    "    return value\n",
    "    \n",
    "result = myfunc(8)\n",
    "\n",
    "global_a, result"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**No confusion!**\n",
    "\n",
    "  \n",
    "  \n",
    "`myfunc` has unique variable names."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### More on functions, loops..."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Controlling loops - `break`**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "for x in lines_in_a_big_file:\n",
    "    if x.startswith('>'):  # this is the only line I want!\n",
    "        do_something(x)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "...waste of time!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "for x in lines_in_a_big_file:\n",
    "    if x.startswith('>'):  # this is the only line I want!\n",
    "        do_something(x)\n",
    "        break  # break the loop\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**<center>break</center>**\n",
    "<center>\n",
    "<img src=\"img/break.png\" alt=\"break\" width=\"50%\"/>\n",
    "</center>\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Controlling loops - `continue`**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "for x in lines_in_a_big_file:\n",
    "    if x.startswith('>'):  # this is a comment\n",
    "        # just skip this! don't do anything\n",
    "    do_something(x)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "for x in lines_in_a_big_file:\n",
    "    if x.startswith('>'):  # this is a comment\n",
    "        continue  # go on to the next iteration\n",
    "    do_something(x)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "for x in lines_in_a_big_file:\n",
    "    if not x.startswith('>'):  # this is *not* a comment\n",
    "        do_something(x)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**<center>continue</center>**\n",
    "<center>\n",
    "<img src=\"img/continue.png\" alt=\"break\" width=\"50%\"/>\n",
    "</center>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Another control statement: pass** - the placeholder"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "def a_function():\n",
    "    # I have not implemented this just yet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "def a_function():\n",
    "    # I have not implemented this just yet\n",
    "    pass\n",
    "\n",
    "a_function()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Returning nothing**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "def a_function():\n",
    "    pass\n",
    "\n",
    "def b_function():\n",
    "    return"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "result_a = a_function()\n",
    "result_b = b_function()\n",
    "print('a:', result_a, 'b:', result_b)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Another keyword: `None`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "Other keywords: `True`, `import`, `and`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "What is `None`? What type? Why?\n",
    "When is it used?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- What is it?\n",
    "   -  A keyword with a constant value (like `True`, `False`) \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Why and when?\n",
    "   - To signal \"emtpy values\"\n",
    "   - Functions that don't return anything meaningful\n",
    "   - Variables with no values yet"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### `None`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "- What type?\n",
    "   - The `NoneType`\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "type(None)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Comparing `None`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "None == True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "None == False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "value = None\n",
    "if value:\n",
    "    print('value is something')\n",
    "else:\n",
    "    print('no value!')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Comparing `None`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "None <= 0 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "myvalue = None\n",
    "if myvalue and myvalue <= 0:\n",
    "    print('The value is smaller than or equal to 0')\n",
    "else:\n",
    "    print('The value is either None or greater to zero')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "**Keyword arguments**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "open('../files/250.imdb', 'r', encoding='utf-8')\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "def prettyprinter(name, value, delim=\":\"):\n",
    "    out = \"The \" + name + \" is \" + delim + \" \" + value + \".\"\n",
    "    return out"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Programmer can set default values"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "<center>\n",
    "<img src=\"img/keywordarg.png\" alt=\"keyword\" width=\"50%\"/>\n",
    "</center>\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"title\", \"Movie\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "- User can ignore the arguments (default value is used)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "```py\n",
    "def prettyprinter(name, value, delim=\":\"):\n",
    "    out = \"The \" + name + \" is \" + delim + \" \" + value + \".\"\n",
    "    return out\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "  prettyprinter(\"genre\", \"Drama\", \"=\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"genre\", \"Drama\", delim=\"=\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "def prettyprinter(name, value, delim=\":\", end=None):\n",
    "    out = \"The \" + name + \" is \" + delim + \" \" + value\n",
    "    if end:\n",
    "        out += end\n",
    "    return out\n",
    "\n",
    "my_str = prettyprinter(\"title\", \"Movie\")\n",
    "print(my_str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"genre\", \"Drama\", \"=\", \".\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"genre\", \"Drama\", delim=\"=\", end=\"!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"genre\", \"Drama\", end=\"!\", delim=\":::\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"genre\", \"Drama\", end=\"!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "prettyprinter(\"genre\", \"Drama\", delim=\"=\", \".\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "**Positional arguments comes first, keyword arguments after!**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "```py\n",
    "open(file, mode='r', buffering=-1, encoding=None, errors=None,\n",
    "     newline=None, closefd=True, opener=None)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Gives better overview"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "open('../files/250.imdb', 'r', encoding='utf-8')\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "open('../files/250.imdb', mode='r', encoding='utf-8')\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "open('../files/250.imdb', encoding='utf-8', mode='r')\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Keyword arguments\n",
    "\n",
    "- programmer: set default values\n",
    "- user: ignore arguments\n",
    "- better overview"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Exercise 1\n",
    "\n",
    "\n",
    "<b>&rarr; Notebook Day_4_Exercise_1  (~30 minutes) </b>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Modules\n",
    "\n",
    "- Use a module\n",
    "- Create a module"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### What is a module?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- a python file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- a organizational unit"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- a library"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Remember?\n",
    "\n",
    "\n",
    "\n",
    "#### Why functions?\n",
    "- Cleaner code\n",
    "- Better defined tasks in code\n",
    "- Re-usability\n",
    "- Better structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Why modules?\n",
    "\n",
    "- Cleaner code\n",
    "- Better defined tasks in code\n",
    "- Re-usability\n",
    "- Better structure\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Collect all related functions in one file\n",
    "- Import a module to use its functions\n",
    "- Only need to understand what the functions do, not how"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Example: **sys**\n",
    "\n",
    "```py\n",
    "import sys\n",
    "\n",
    "sys.argv[1]\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Python standard modules\n",
    "\n",
    "Check out the [module index](https://docs.python.org/3.6/py-modindex.html)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "How to find the right module?\n",
    "\n",
    "How to understand it?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "How to find the right module?\n",
    "\n",
    "- look at the module index\n",
    "- search [PyPI](http://pypi.org)\n",
    "- ask your colleagues\n",
    "- search the web!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "How to understand it?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "import math\n",
    "\n",
    "help(math)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "dir(math)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "help(math.sqrt)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    " math.sqrt(3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Different ways of importing"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Standard:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "import math"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "math.sqrt(3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Alias:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "import math as m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "m.sqrt(3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "import math as c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "counter = c.Counter()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Get access to only one function:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "from math import sqrt, ceil"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "sqrt(3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### When?\n",
    "\n",
    "- `import math`: standard\n",
    "- `import xml.etree.ElementTree as ET`: for long names\n",
    "- `from collections import defaultdict`: import only one function/class"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Exercise\n",
    "\n",
    "\n",
    "\n",
    "<b>&rarr; Notebook Day_4_Exercise_2  (~30 minutes) </b>\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Documentation and commenting your code\n",
    "\n",
    "\n",
    "Remember `help()`?\n",
    "\n",
    "Works because somebody else has documented their code!\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "def process_file(filename, chrom, pos):\n",
    "    for line in open(filename):\n",
    "        if not line.startswith('#'):\n",
    "            columns = line.split('\\t')\n",
    "            if col[0] == chrom and col[1] == pos:\n",
    "                print(line)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "**?**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "def process_file(filename, chrom, pos):\n",
    "    \"\"\"\n",
    "    Reads a vcf file and prints the genotype of the samples\n",
    "    at chromosome chrom and position pos.\n",
    "    \"\"\"\n",
    "    for line in open(filename):\n",
    "        if not line.startswith('#'):\n",
    "            columns = line.split('\\t')\n",
    "            if col[0] == chrom and col[1] == pos:\n",
    "                print(line)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "help(process_file)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "Your code may have two types of users:\n",
    "\n",
    "- library users\n",
    "- maintainers (maybe yourself!)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "Write documentation for both of them!\n",
    "\n",
    "- library users:` \"\"\" What does this function do? \"\"\"` (doc strings)\n",
    "- maintainers:    `   # implementation details`        (comments)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "def process_file(filename, chrom, pos):\n",
    "    \"\"\"\n",
    "    Reads a vcf file and prints the genotypes of corresponding to\n",
    "    chromosome chrom and position pos.\n",
    "    \"\"\"\n",
    "    for line in open(filename):\n",
    "        if not line.startswith('#'):  # skip comments\n",
    "            columns = line.split('\\t')  # file is tab separated\n",
    "            # Check if chrom and pos match\n",
    "            if col[0] == chrom and col[1] == pos:\n",
    "                # genotype starts at column index 9\n",
    "                print(col[9:])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Read more:\n",
    "\n",
    "https://realpython.com/documenting-python-code/\n",
    "\n",
    "https://www.python.org/dev/peps/pep-0008/?#comments\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Your own code as a module\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- Put your code in a file\n",
    "- Document it\n",
    "- Write a main function?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Documentation:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    " - At the beginning of the file\n",
    " \n",
    "   `\"\"\" This module provides functions for...\"\"\"`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    " - For every function\n",
    " \n",
    "    <pre>def make_list(x):    \n",
    "        \"\"\" Returns an list of lenght x \"\"\"</pre>\n",
    "        "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Comments:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    " - Wherever the code is hard to understand\n",
    " \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "my_list[5] += other_list[3]  # explain why you do this!```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Using your module\n",
    "\n",
    "- Save your code in `mymodule.py`\n",
    "\n",
    "- Run it: `python3 mymodule.py`\n",
    "\n",
    "- Import it: `>>> import mymodule`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### The main function"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "```py\n",
    "\n",
    "def main(input_str):\n",
    "    # do something\n",
    "    pass\n",
    "    \n",
    "# at the end of the file\n",
    "if __name__ == \"__main__\":\n",
    "   result = main(sys.argv[1])        # get input from command line\n",
    "   print(\"The result is: \", result)  # show result to user\n",
    "```\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- When the module is run a a script: read input, print output\n",
    "- When the module is imported: get access to `main()`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### The main function"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "**In file** `module.py`**:**\n",
    "\n",
    "\n",
    "--------------\n",
    "```py\n",
    "print(\"My name is \" + __name__)\n",
    "\n",
    "if __name__ == \"__main__\":\n",
    "    print(\"I'm run as a main module\")\n",
    "```\n",
    "------------"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "import module as m"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "source": [
    "But if we run the file `module.py` as a script:\n",
    "\n",
    "<img src=\"img/run_main.png\" alt=\"mainmodule\" style=\"width: 40%\"/>\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "###### Summary\n",
    "\n",
    "\n",
    "\n",
    "<b>&rarr; Notebook Day_4_Exercise_3  (~30 minutes) </b>\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Using somebody else's code\n",
    "\n",
    "\n",
    "Written by last year's teacher, Frédéric Haziza (slightly modified).\n",
    "\n",
    "\n",
    "Lets you work with a database with information about real estate around Uppsala.\n",
    "\n",
    "Have a look at [the documentation](../files/db_module_documentation.html) and\n",
    "the [the code](../exercises/day4/db.py)!\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## A lot of new things!\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- classes\n",
    "\n",
    "```py\n",
    "class HomeEntry():\n",
    "    def __init__(self, row):\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- methods\n",
    "\n",
    "```py\n",
    "    return self.raw_query(q)\n",
    "```\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- javascript!\n",
    "\n",
    "```js\n",
    "   function createPopup(feature) {\n",
    "     feature.popup = new OpenLayers.Popup.FramedCloud(\"pop\",\n",
    "     ...\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "- ..."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "**You don't need to understand these things, as long as you can understand the documentation!**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### The database\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- A house:\n",
    "    - a `HomeEntry`\n",
    "    - id, type, location, adress, date, asked_price, price, rooms, area, rent, latitude, longitude\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- What you need\n",
    "    - **latitude**, **longitude**, **price**, **area**\n",
    "    - `home.get_price()`, `home.get_location()`, `home.get_area()`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Getting houses from the database"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "database = HomeDB('uppsala.sqlite')\n",
    "database.connect()```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "homes = db.select()  # Get everything```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "homes = db.select('price > 1000000')  # Select by some criteria```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "homes = db.select('id = \"2447\"')\n",
    "    ```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### The magic - printing maps"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "`plot()` creates a html file, which you can open in a browser."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```py\n",
    "plot(selection,                    # a list of homes to print\n",
    "     output='selection.html',      # the name of the output file\n",
    "     special=None,                 # a very special house\n",
    "     zoom=12,                      # the zoom levl\n",
    "     latitude=59.83732598851705,   # the center position (lat(\n",
    "     longitude=17.64549846959149,  # the center position (long)\n",
    "     radius=5000)                  # circle radius\n",
    "     ```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- `selection`\n",
    "- `output`\n",
    "- `special`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Your program\n",
    "\n",
    "- get a collection of houses\n",
    "- sort and organize them\n",
    "- plot them"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "**Other useful functions**\n",
    "- `haversine()`\n",
    "- `sort_by_price()`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Exercise 4\n",
    "\n",
    "\n",
    "<b>&rarr; Notebook Day_4_Exercise_4  (~60 minutes) </b>\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Sum-up day 4"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- control statements: `break`, `continue`, `pass`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- `None`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- scope: global and local. Be careful with your variable names!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- keyword arguments: `open(filename, encoding=\"utf-8\")`\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Sum-up day 4"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "- importing: Python standard modules, your own modules...\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "- documentation: `help()`, `\"\"\"Doc string\"\"\"`, `# comment`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "\n",
    "- main function: what is run when"
   ]
  }
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