20230510 TRAN Transitions and Transversions.ipynb

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    "def  transition_transversion_ratio(s1,s2):\n",
    "    \"\"\"return the transition_transversion_ratio of two strings with same length\"\"\"\n",
    "    transition_number = 0\n",
    "    transversion_number = 0\n",
    "    transition_case_list = [\"AG\",\"GA\",\"CT\",\"TC\"]\n",
    "    transversion_case_list = [\"AT\",\"TA\",\"AC\",\"CA\",\"CG\",\"GC\",\"GT\",\"TG\"]\n",
    "    if len(s1) != len(s2):\n",
    "        return print(\"the length of s1 not equal to s2\")\n",
    "    else:\n",
    "        for i in range(len(s1)):\n",
    "            if s1[i]==s2[i]:\n",
    "                continue\n",
    "            elif s1[i]+s2[i] in transition_case_list:\n",
    "                transition_number+=1\n",
    "            elif s1[i]+s2[i] in transversion_case_list:\n",
    "                transversion_number+=1\n",
    "    return transition_number/transversion_number"
   ]
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    {
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      ]
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     "execution_count": 6,
     "metadata": {},
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   ],
   "source": [
    "from Bio import SeqIO\n",
    "seq_string = []\n",
    "filename= \"rosalind_tran.txt\"\n",
    "dictionary= \"D:\\\\\"\n",
    "with open(dictionary+filename, \"r\") as fa:\n",
    "    for seq_record in SeqIO.parse(fa,\"fasta\"):\n",
    "        seq_string.append(str(seq_record.seq))\n",
    "s1 = seq_string[0]\n",
    "s2 = seq_string[1]\n",
    "transition_transversion_ratio(s1,s2)"
   ]
  },
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   "id": "4d649478",
   "metadata": {},
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