translation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# DNA Translation  ⇒ DNA to Protein\n",
    "**Translation Theory : DNA ⇒ RNA ⇒ Protein**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Tasks\n",
    "1. Manually download DNA and Protein(to check our solution) sequence from NCBI.\n",
    "2. Import DNA data into Python \n",
    "3. Create an algorithm for DNA translation\n",
    "4. Check if translation matches your dowloaded protein sequence"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Task-1: Manually Download Sequence File\n",
    "- Go to NCBI and select Nucleotide database \n",
    "- Enter the accession code, **NM_207618.2**\n",
    "- Click on **FASTA**\n",
    "- Copy and paste(without sequence info) the sequence into a text editor.\n",
    "- Save both sequence as text file(.txt) into a folder called **data**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Task-2: Import DNA Sequence Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "inputfile = \"../data/dna.txt\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read the DNA sequence file \n",
    "f = open(inputfile, \"r\")\n",
    "seq = f.read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCA\\nGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCT\\nCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCT\\nTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCT\\nCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTG\\nAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAA\\nACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAA\\nGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGAT\\nTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCA\\nGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGA\\nCCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTT\\nTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATT\\nGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGG\\nTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTT\\nGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTC\\nACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTG\\nATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT\\n\\n'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# To see the DNA sequence \n",
    "seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1175"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Check length of DNA seq.\n",
    "len(seq)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> The sequence length is not correct! the original size of this sequence is 1157. The 18 characters are the special characters like **\\n**(new line), **\\r**(tab). The special characters affect the sequence quality and increase the size of this sequence. So, we have to process/clean this sequence file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCA\n",
      "GATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCT\n",
      "CCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCT\n",
      "TAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCT\n",
      "CAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTG\n",
      "AGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAA\n",
      "ACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAA\n",
      "GGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGAT\n",
      "TTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCA\n",
      "GTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGA\n",
      "CCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTT\n",
      "TATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATT\n",
      "GCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGG\n",
      "TCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTT\n",
      "GCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTC\n",
      "ACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTG\n",
      "ATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Print the DNA sequence \n",
    "print(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# New lines replace with empty space to remove the extra characters from sequence file  \n",
    "seq = seq.replace(\"\\n\", \"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT'"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1157"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Check sequence length again! \n",
    "len(seq)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "That's correct! same as NCBI."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT\n"
     ]
    }
   ],
   "source": [
    "# To see sequence again\n",
    "print(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Tabs replace with empty space to remove extra character from sequence file \n",
    "seq = seq.replace(\"\\r\", \"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1157"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT\n"
     ]
    }
   ],
   "source": [
    "print(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Codon table for translation\n",
    "table = { \n",
    "        'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', \n",
    "        'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', \n",
    "        'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', \n",
    "        'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',                  \n",
    "        'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', \n",
    "        'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', \n",
    "        'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', \n",
    "        'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', \n",
    "        'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', \n",
    "        'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', \n",
    "        'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', \n",
    "        'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', \n",
    "        'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', \n",
    "        'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L', \n",
    "        'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_', \n",
    "        'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W', \n",
    "    }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# To see the table \n",
    "table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'CAA' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-14-0fb9e6e3dc2d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# Lookup\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mtable\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mCAA\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m: name 'CAA' is not defined"
     ]
    }
   ],
   "source": [
    "# Lookup / Extract infromation from the codon table \n",
    "table[CAA]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Error occurs, because \"CCA\" is a string but we tried to access without quote. That's why Python interpreter give an error."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Q'"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Extract \"CCA\"\n",
    "table[\"CAA\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'P'"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "table[\"CCT\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Task-3: Create an Algorithm\n",
    "- Step-1: Check the length of sequence is divisible by 3.\n",
    "- Step-2: Look each 3 letter strings in table and store result.\n",
    "- Step-3: Continue lookups untill reading end of sequence."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "protein = \"\"\n",
    "if len(seq) % 3 == 0: \n",
    "    for i in range(0, len(seq), 3):\n",
    "        codon = seq[i:i+3]\n",
    "        protein += table[codon]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create a function to translate DNA sequence into protein."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "def translate(seq): \n",
    "    \"\"\"\n",
    "    Reads sequence file as input. Transcribe input sequence file into RNA, then translate into Protein.\n",
    "    \"\"\"\n",
    "    \n",
    "    table = { \n",
    "        'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', \n",
    "        'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', \n",
    "        'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', \n",
    "        'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',                  \n",
    "        'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', \n",
    "        'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', \n",
    "        'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', \n",
    "        'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', \n",
    "        'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', \n",
    "        'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', \n",
    "        'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', \n",
    "        'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', \n",
    "        'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', \n",
    "        'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L', \n",
    "        'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_', \n",
    "        'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W', \n",
    "    }\n",
    "    \n",
    "    protein = \"\"\n",
    "    if len(seq) % 3 == 0: \n",
    "        for i in range(0, len(seq), 3):\n",
    "            codon = seq[i:i+3]\n",
    "            protein += table[codon]\n",
    "    return protein\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'I'"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Test translate function\n",
    "translate(\"ATA\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'S'"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "translate(\"TCA\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "def translate(seq): \n",
    "    \"\"\"\n",
    "    Reads sequence file as input. Transcribe input sequence file into RNA, then translate into Protein.\n",
    "    \"\"\"\n",
    "    \n",
    "    table = { \n",
    "        'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', \n",
    "        'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', \n",
    "        'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', \n",
    "        'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',                  \n",
    "        'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', \n",
    "        'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', \n",
    "        'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', \n",
    "        'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', \n",
    "        'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', \n",
    "        'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', \n",
    "        'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', \n",
    "        'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', \n",
    "        'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', \n",
    "        'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L', \n",
    "        'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_', \n",
    "        'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W', \n",
    "    }\n",
    "    \n",
    "    protein = \"\"\n",
    "    if len(seq) % 3 == 0: \n",
    "        for i in range(0, len(seq), 3):\n",
    "            codon = seq[i:i+3]\n",
    "            protein += table[codon]\n",
    "    return protein\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on function translate in module __main__:\n",
      "\n",
      "translate(seq)\n",
      "    Reads sequence file as input. Transcribe input sequence file into RNA, then translate into Protein.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(translate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'A'"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "translate(\"GCC\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CCTGAAAACC'"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Slicing sequence \n",
    "seq[40:50]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create a function to read sequence file "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "def read_seq(inputfile): \n",
    "    \"\"\"Reads and returns the input sequences with special characters removed\"\"\"\n",
    "    with open(inputfile, \"r\") as f: \n",
    "        seq = f.read() \n",
    "    seq = seq.replace(\"\\n\", \"\")\n",
    "    seq = seq.replace(\"\\r\", \"\") \n",
    "    \n",
    "    return seq "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read DNA sequence by using read_seq() function\n",
    "dna = read_seq(\"../data/dna.txt\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "''"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Call translate function\n",
    "translate(dna)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " >Python gives us empty string! because **sequence is not divisible by 3**. NCBI translation starts with 21 and ends with 938. but in Python translation should start at 20 position and end at 938"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Empty string cause of length problem\n",
    "len(seq) % 3 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MSTHDTSLKTTEEVAFQIILLCQFGVGTFANVFLFVYNFSPISTGSKQRPRQVILRHMAVANALTLFLTIFPNNMMTFAPIIPQTDLKCKLEFFTRLVARSTNLCSTCVLSIHQFVTLVPVNSGKGILRASVTNMASYSCYSCWFFSVLNNIYIPIKVTGPQLTDNNNNSKSKLFCSTSDFSVGIVFLRFAHDATFMSIMVWTSVSMVLLLHRHCQRMQYIFTLNQDPRGQAETTATHTILMLVVTFVGFYLLSLICIIFYTYFIYSHHSLRHCNDILVSGFPTISPLLLTFRDPKGPCSVFFNC_'"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Call translation from 20 to 938\n",
    "translate(dna[20:938])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Task-4: Comparison"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Read protein sequence\n",
    "prt = read_seq(\"../data/protein.txt\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MSTHDTSLKTTEEVAFQIILLCQFGVGTFANVFLFVYNFSPISTGSKQRPRQVILRHMAVANALTLFLTIFPNNMMTFAPIIPQTDLKCKLEFFTRLVARSTNLCSTCVLSIHQFVTLVPVNSGKGILRASVTNMASYSCYSCWFFSVLNNIYIPIKVTGPQLTDNNNNSKSKLFCSTSDFSVGIVFLRFAHDATFMSIMVWTSVSMVLLLHRHCQRMQYIFTLNQDPRGQAETTATHTILMLVVTFVGFYLLSLICIIFYTYFIYSHHSLRHCNDILVSGFPTISPLLLTFRDPKGPCSVFFNC'"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Not identical cause of stop codon\n",
    "prt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MSTHDTSLKTTEEVAFQIILLCQFGVGTFANVFLFVYNFSPISTGSKQRPRQVILRHMAVANALTLFLTIFPNNMMTFAPIIPQTDLKCKLEFFTRLVARSTNLCSTCVLSIHQFVTLVPVNSGKGILRASVTNMASYSCYSCWFFSVLNNIYIPIKVTGPQLTDNNNNSKSKLFCSTSDFSVGIVFLRFAHDATFMSIMVWTSVSMVLLLHRHCQRMQYIFTLNQDPRGQAETTATHTILMLVVTFVGFYLLSLICIIFYTYFIYSHHSLRHCNDILVSGFPTISPLLLTFRDPKGPCSVFFNC'"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "translate(dna[20:935])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MSTHDTSLKTTEEVAFQIILLCQFGVGTFANVFLFVYNFSPISTGSKQRPRQVILRHMAVANALTLFLTIFPNNMMTFAPIIPQTDLKCKLEFFTRLVARSTNLCSTCVLSIHQFVTLVPVNSGKGILRASVTNMASYSCYSCWFFSVLNNIYIPIKVTGPQLTDNNNNSKSKLFCSTSDFSVGIVFLRFAHDATFMSIMVWTSVSMVLLLHRHCQRMQYIFTLNQDPRGQAETTATHTILMLVVTFVGFYLLSLICIIFYTYFIYSHHSLRHCNDILVSGFPTISPLLLTFRDPKGPCSVFFNC'"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "prt "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Comparison\n",
    "prt == translate(dna[20:935])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Exclude the last character\n",
    "prt == translate(dna[20:938])[:-1]"
   ]
  }
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