{
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   "cell_type": "markdown",
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   "source": [
    "# Lesson 1c: Conditionals\n",
    "\n",
    "**Conditionals** are used to tell your computer to do a set of instructions depending on whether or not a Boolean is `True`. In other words, we are telling the computer:\n",
    "\n",
    "    if something is true:\n",
    "        do task a\n",
    "    otherwise:\n",
    "        do task b\n",
    "\n",
    "In fact, the syntax in Python is almost exactly the same. As an example, let's ask whether or not a codon is the canonical start codon (`AUG`)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This codon is the start codon.\n"
     ]
    }
   ],
   "source": [
    "codon = 'AUG'\n",
    "\n",
    "if codon == 'AUG':\n",
    "    print('This codon is the start codon.')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The syntax of the `if` statement is apparent in the above example. The Boolean expression, `codon == 'AUG'`, is called the **condition**. If it is `True`, the indented statement below it is executed.  This brings up a very important aspect of Python syntax.\n",
    "\n",
    "<div class=\"alert alert-info\">\n",
    "\n",
    "<center>Indentation matters.</center>\n",
    "\n",
    "</div>\n",
    "\n",
    "    \n",
    "Any lines with the same level of indentation will be evaluated together."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This codon is the start codon.\n",
      "Same level of intentation, so still printed!\n"
     ]
    }
   ],
   "source": [
    "codon = 'AUG'\n",
    "\n",
    "if codon == 'AUG':\n",
    "    print('This codon is the start codon.')\n",
    "    print('Same level of intentation, so still printed!')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "What happens if our codon is not the start codon?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "codon = 'AGG'\n",
    "\n",
    "if codon == 'AUG':\n",
    "    print('This codon is the start codon.')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Nothing is printed. This is because we did not tell Python what to do if the Boolean expression `codon == 'AUG'` evaluated `False`. We can add that with an **`else`** **clause** in the conditional."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This codon is not the start codon.\n"
     ]
    }
   ],
   "source": [
    "codon = 'AGG'\n",
    "\n",
    "if codon == 'AUG':\n",
    "    print('This codon is the start codon.')\n",
    "else:\n",
    "    print('This codon is not the start codon.')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Great!  Now, we have a construction that can choose which action to take depending on a value. So, if we're zooming along an RNA sequence, we could pick out the start codon and infer where translation would start. Now, what if we want to know if we hit a canonical stop codon (`UAA`, `UAG`, or `UGA`)?  We can nest the conditionals!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This codon is a stop codon.\n"
     ]
    }
   ],
   "source": [
    "codon = 'UAG'\n",
    "\n",
    "if codon == 'AUG':\n",
    "    print('This codon is the start codon.')\n",
    "else:\n",
    "    if codon == 'UAA' or codon == 'UAG' or codon == 'UGA':\n",
    "        print('This codon is a stop codon.')\n",
    "    else:\n",
    "        print('This codon is neither a start nor stop codon.')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Notice that the indentation defines which clause the statement belongs to. E.g., the second `if` statement is executed as part of the first `else` clause.\n",
    "\n",
    "We can be more concise and avoid the nesting by using an `elif` clause."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This codon is neither a start nor stop codon.\n"
     ]
    }
   ],
   "source": [
    "codon = 'UGG'\n",
    "\n",
    "if codon == 'AUG':\n",
    "    print('This codon is the start codon.')\n",
    "elif codon == 'UAA' or codon == 'UAG' or codon == 'UGA':\n",
    "    print('This codon is a stop codon.')\n",
    "else:\n",
    "    print('This codon is neither a start nor stop codon.')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Computing environment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPython 3.7.4\n",
      "IPython 7.8.0\n",
      "\n",
      "jupyterlab 1.1.3\n"
     ]
    }
   ],
   "source": [
    "%load_ext watermark\n",
    "%watermark -v -p jupyterlab"
   ]
  }
 ],
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