{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Exercise 3.1: Using string methods\n",
    "\n",
    "<hr>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In [Lesson 7](l07_intro_to_functions.ipynb), we wrote a function to compute the reverse complement of a sequence.  \n",
    "\n",
    "**a)** Write that function again, still using a `for` loop, but do not use the built-in `reversed()` function.\n",
    "\n",
    "**b)** Write the function one more time, but without any loops."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<br />"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Solution\n",
    "\n",
    "**a)** The trick here is to do what we did in Lesson 7, except use `[::-1]` indexing instead of the `reversed()` function."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "def complement_base(base):\n",
    "    \"\"\"Returns the Watson-Crick complement of a base.\"\"\"\n",
    "    if base == 'A' or base == 'a':\n",
    "        return 'T'\n",
    "    elif base == 'T' or base == 't':\n",
    "        return 'A'\n",
    "    elif base == 'G' or base == 'g':\n",
    "        return 'C'\n",
    "    else:\n",
    "        return 'G'\n",
    "\n",
    "\n",
    "def reverse_complement(seq):\n",
    "    \"\"\"Compute reverse complement of a sequence.\"\"\"\n",
    "    # Initialize reverse complement\n",
    "    rev_seq = ''\n",
    "    \n",
    "    # Loop through and populate list with reverse complement\n",
    "    for base in seq:\n",
    "        rev_seq += complement_base(base)\n",
    "        \n",
    "    return rev_seq[::-1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And we'll do a quick test with the same sequence as in lesson 7."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'TGCAACTGC'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "reverse_complement('GCAGTTGCA')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Bingo!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**b)** We can eliminate the **`for`** loop by using the `replace()` method of strings."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def reverse_complement(seq):\n",
    "    \"\"\"Compute reverse complement of a sequence.\"\"\"\n",
    "    # Initialize rev_seq to a lowercase seq\n",
    "    rev_seq = seq.lower()\n",
    "    \n",
    "    # Substitute bases\n",
    "    rev_seq = rev_seq.replace('t', 'A')\n",
    "    rev_seq = rev_seq.replace('a', 'T')\n",
    "    rev_seq = rev_seq.replace('g', 'C')\n",
    "    rev_seq = rev_seq.replace('c', 'G')\n",
    "    \n",
    "    return rev_seq[::-1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And let's give it a test!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'TGCAACTGC'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "reverse_complement('GCAGTTGCA')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Note:** We haven't learned about it yet, but some Googling would allow you to use the `translate()` and `maketrans()` string methods. `maketrans()` makes a **translation table** for characters in a string, and then the `translate()` functions uses it to mutate the characters in the list."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'TGCAACTGC'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def reverse_complement(seq):\n",
    "    \"\"\"Compute reverse complement of a sequence.\"\"\"\n",
    "    return seq.translate(str.maketrans('ATGCatgc', 'TACGTACG'))[::-1]\n",
    "\n",
    "reverse_complement('GCAGTTGCA')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "So, we were able to do it in one line!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Computing environment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPython 3.7.7\n",
      "IPython 7.13.0\n",
      "\n",
      "jupyterlab 1.2.6\n"
     ]
    }
   ],
   "source": [
    "%load_ext watermark\n",
    "%watermark -v -p jupyterlab"
   ]
  }
 ],
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   "codemirror_mode": {
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