20230426 Open Reading Frames.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 52,
   "id": "deed2530",
   "metadata": {},
   "outputs": [],
   "source": [
    "def call_ORF(seq):\n",
    "    \"\"\"return a list of sub_seq that be called as ORF, \n",
    "    from both the sense starnd and the reverse complement.\"\"\"\n",
    "    start_code= [\"ATG\"]\n",
    "    end_code = ['TAA', 'TAG', 'TGA']\n",
    "    ORF_list = []\n",
    "    for i in range(len(seq)):\n",
    "        if i+3 <= len(seq) and seq[i:i+3]==start_code[0]:\n",
    "            #print(i)\n",
    "            for j in range(i+3,len(seq),3):\n",
    "                if seq[j:j+3] in end_code:\n",
    "                    ORF_call = seq[i:j+3]\n",
    "                    ORF_list.append(ORF_call)\n",
    "                    break\n",
    "    #print(ORF_list)                \n",
    "    \"\"\"remove the replicate seq in ORF_list\"\"\"\n",
    "#     redundant_list = []\n",
    "#     for seq in ORF_list:\n",
    "#         for compare in ORF_list:\n",
    "#             if seq in compare and seq != compare:\n",
    "#                 redundant_list.append(seq)\n",
    "#     ORF_list = list(set(ORF_list)-set(redundant_list))\n",
    "    return ORF_list\n",
    "        \n",
    "\n",
    "def complement_DNA(seq):\n",
    "    \"\"\"return the reverse complement DNA\"\"\"\n",
    "    complement_seq = \"\"\n",
    "    complement_code={\"A\":\"T\",\"T\":\"A\",\"C\":\"G\",\"G\":\"C\"}\n",
    "    for i in range(len(seq)-1, -1, -1):\n",
    "        complement_seq+=complement_code[seq[i]]\n",
    "    return complement_seq\n",
    "\n",
    "\n",
    "def call_ORF_frombothstrand(seq):\n",
    "    ORF_list = []\n",
    "    complement_seq = complement_DNA(seq)\n",
    "    ORF_list= call_ORF(seq) + call_ORF(complement_seq)\n",
    "    return ORF_list\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "id": "cd28b0c4",
   "metadata": {},
   "outputs": [],
   "source": [
    "seq=\"TTTTCGAATGAACCATCGGGCAAATGAGGACCTATCCTGGGTTTGACACTTAGCTATCATGACGGCAGCTTGCTGCATGGGCATAAGGGGTTGACGGTAGTTGCATCTCTGCCGTTTAGAGAAAAGTTTCGTGTGGGGATAGGATCAGGACCCGAAGCGGGTGTAACGTGCTCTTCCGTTTGGCTTGACACTCACGTAGTTTTGGGAGACCAATTTTGACCTCCAGTTTTATTATCCCTTTCTTACTAGGTACGGAGAAGCATGGACGCTCACGCTCTTCTTGGTGAATTTTGGTCACTATAGATACTATGGGATCTGGGTAACAAAGACGTAGCTTACTTCCCCTGCACACGTTCAATCCCTCGGTTGTGAAGGTTGCCTAAACTAAACTTTCCCGTGTCTGGCCTGACCACGATTTTGTTCTTCTTTACGCCAAGTAACAGAACTAGCTCATGACGGCTAGCGTCACAATATAGCTATATTGTGACGCTAGCCGTCATCCTTGGTGGGAAGCTCTACACTTTCTGACGCATCCTACAAGAGTCGACTTCCGTCCTAAGTGAAGTTTGATCTGATCCCGTCCACGACGCTAAGTTCCTTCTGGGCCGCGAATGTCTCTAGGGTTTCCCAGAACCCGCCTACGTAGCTGCCATTTAACCCGGTCCGCGGATTGGTAGAGAATCGTTGGAATCCCAATTCAATCTTGCTCTACCTCTCGAACCGCAACTCGTTCCTGCAGAAACTTAACTTGTGAGACCTGAGGTGTCCCCTGAGTTCAGATAGTCCACTAAGCTATTCCAATTGTCGTCCGAGGAACATGGGCTGGACTAAAACGGAAGAAGGGTGCAAACTGACTCAACTAAGCCGGCTGGGACGTCAAACACAGCCGAAGCCATCGCGAGTTAGTCTGCCCGCGTGTCACCGCCCTTCGCCAAACAGATGCGATAGCCCT\"\n",
    "testlist= call_ORF_frombothstrand(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "id": "23603790",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'TTT': 'F',\n",
       " 'TTC': 'F',\n",
       " 'TTA': 'L',\n",
       " 'TTG': 'L',\n",
       " 'CTT': 'L',\n",
       " 'CTC': 'L',\n",
       " 'CTA': 'L',\n",
       " 'CTG': 'L',\n",
       " 'TCT': 'S',\n",
       " 'TCC': 'S',\n",
       " 'TCA': 'S',\n",
       " 'TCG': 'S',\n",
       " 'AGT': 'S',\n",
       " 'AGC': 'S',\n",
       " 'TAT': 'Y',\n",
       " 'TAC': 'Y',\n",
       " 'TAA': '*',\n",
       " 'TAG': '*',\n",
       " 'TGA': '*',\n",
       " 'TGT': 'C',\n",
       " 'TGC': 'C',\n",
       " 'TGG': 'W',\n",
       " 'CCT': 'P',\n",
       " 'CCC': 'P',\n",
       " 'CCA': 'P',\n",
       " 'CCG': 'P',\n",
       " 'CAT': 'H',\n",
       " 'CAC': 'H',\n",
       " 'CAA': 'Q',\n",
       " 'CAG': 'Q',\n",
       " 'CGT': 'R',\n",
       " 'CGC': 'R',\n",
       " 'CGA': 'R',\n",
       " 'CGG': 'R',\n",
       " 'AGA': 'R',\n",
       " 'AGG': 'R',\n",
       " 'GTT': 'V',\n",
       " 'GTC': 'V',\n",
       " 'GTA': 'V',\n",
       " 'GTG': 'V',\n",
       " 'GCT': 'A',\n",
       " 'GCC': 'A',\n",
       " 'GCA': 'A',\n",
       " 'GCG': 'A',\n",
       " 'GAT': 'D',\n",
       " 'GAC': 'D',\n",
       " 'GAA': 'E',\n",
       " 'GAG': 'E',\n",
       " 'GGT': 'G',\n",
       " 'GGC': 'G',\n",
       " 'GGA': 'G',\n",
       " 'GGG': 'G',\n",
       " 'ATT': 'I',\n",
       " 'ATC': 'I',\n",
       " 'ATA': 'I',\n",
       " 'ATG': 'M',\n",
       " 'ACT': 'T',\n",
       " 'ACC': 'T',\n",
       " 'ACA': 'T',\n",
       " 'ACG': 'T',\n",
       " 'AAT': 'N',\n",
       " 'AAC': 'N',\n",
       " 'AAA': 'K',\n",
       " 'AAG': 'K'}"
      ]
     },
     "execution_count": 60,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "codons = {'F': ['UUU', 'UUC'],\n",
    "  'L': ['UUA', 'UUG', 'CUU', 'CUC', 'CUA', 'CUG'],\n",
    "  'S': ['UCU', 'UCC', 'UCA', 'UCG', 'AGU', 'AGC'],\n",
    "  'Y': ['UAU', 'UAC'],\n",
    "  '*': ['UAA', 'UAG', 'UGA'],\n",
    "  'C': ['UGU', 'UGC'],\n",
    "  'W': ['UGG'],\n",
    "  'P': ['CCU', 'CCC', 'CCA', 'CCG'],\n",
    "  'H': ['CAU', 'CAC'],\n",
    "  'Q': ['CAA', 'CAG'],\n",
    "  'R': ['CGU', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'],\n",
    "  'V': ['GUU', 'GUC', 'GUA', 'GUG'],\n",
    "  'A': ['GCU', 'GCC', 'GCA', 'GCG'],\n",
    "  'D': ['GAU', 'GAC'],\n",
    "  'E': ['GAA', 'GAG'],\n",
    "  'G': ['GGU', 'GGC', 'GGA', 'GGG'],\n",
    "  'I': ['AUU', 'AUC', 'AUA'],\n",
    "  'M': ['AUG'],\n",
    "  'T': ['ACU', 'ACC', 'ACA', 'ACG'],\n",
    "  'N': ['AAU', 'AAC'],\n",
    "  'K': ['AAA', 'AAG']}\n",
    "\n",
    "def change_U_to_A(seq):\n",
    "    return seq.replace(\"U\",\"T\")\n",
    "\n",
    "translation_code={}\n",
    "for key, item in codons.items():\n",
    "    for code in item:\n",
    "        translation_code[change_U_to_A(code)]=key\n",
    "        \n",
    "translation_code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "id": "1cc6b9ed",
   "metadata": {},
   "outputs": [],
   "source": [
    "def translate(seq_list):\n",
    "    translation_list=[]\n",
    "    for seq in seq_list:\n",
    "        protein_seq = \"\"\n",
    "        for i in range(0,len(seq),3):\n",
    "            protein_seq += translation_code[seq[i:i+3]]\n",
    "        \n",
    "        if protein_seq[-1]==\"*\":\n",
    "            translation_list.append(protein_seq[:-1])\n",
    "        else:\n",
    "            translation_list.append(protein_seq)\n",
    "            \n",
    "            \n",
    "    return list(set(translation_list))\n",
    "        \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "id": "c388732d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MRQKV\n",
      "MASAVFDVPAGLVESVCTLLPF\n",
      "MSLGFPRTRLRSCHLTRSADW\n",
      "MTAACCMGIRG\n",
      "MTASVTI\n",
      "MAAT\n",
      "MLLRT\n",
      "MS\n",
      "MRTYPGFDT\n",
      "MNHRANEDLSWV\n",
      "MGIRG\n",
      "MR\n",
      "MFLGRQLE\n",
      "MGSG\n",
      "MQLPSTPYAHAASCRHDS\n",
      "MDAHALLGEFWSL\n"
     ]
    }
   ],
   "source": [
    "for seq in translate(testlist):\n",
    "    print(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d1a43f2b",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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