Find_RE_cutting_2_plasmids.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'\\nThis script takes two DNA sequences as input\\nand returns the name of the restriction enzymes able to cut BOTH sequences exactly N times.\\nIt is possible to specify how many times a restriction enzymes is supposed to cut each sequence.\\n\\nVersion      : 1.0\\nRequirements : Python >= 2.7 ; biopython\\nLast edit    : February 1 2018\\nauthor       : alessio.marcozzi@gmail.com\\n'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'''\n",
    "This script takes two DNA sequences as input\n",
    "and returns the name of the restriction enzymes able to cut BOTH sequences exactly N times.\n",
    "It is possible to specify how many times a restriction enzymes is supposed to cut each sequence.\n",
    "\n",
    "Version      : 1.0\n",
    "Requirements : Python >= 2.7 ; biopython\n",
    "Last edit    : February 1 2018\n",
    "author       : alessio.marcozzi@gmail.com\n",
    "'''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: biopython in /Users/amarcozzi/miniconda3/lib/python3.6/site-packages\r\n",
      "Requirement already satisfied: numpy in /Users/amarcozzi/miniconda3/lib/python3.6/site-packages (from biopython)\r\n"
     ]
    }
   ],
   "source": [
    "##Play this cell only to install biopython\n",
    "!pip install biopython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import Restriction\n",
    "from Bio.Seq import Seq\n",
    "from __future__ import print_function #in case of Python 2.7"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "##Insert your \"Plasmid 1\" sequence\n",
    "\n",
    "p1 = '''\n",
    "caggtggcacttttcggggaaatgtgcgcggaacccctatttgtttatttttctaaatacattcaaatatgtatccgctc\n",
    "atgagacaataaccctgataaatgcttcaataatattgaaaaaggaagagtatgagtattcaacatttccgtgtcgccct\n",
    "tattcccttttttgcggcattttgccttcctgtttttgctcacccagaaacgctggtgaaagtaaaagatgctgaagatc\n",
    "agttgggtgcacgagtgggttacatcgaactggatctcaacagcggtaagatccttgagagttttcgccccgaagaacgt\n",
    "tttccaatgatgagcacttttaaagttctgctatgtggcgcggtattatcccgtattgacgccgggcaagagcaactcgg\n",
    "tcgccgcatacactattctcagaatgacttggttgagtactcaccagtcacagaaaagcatcttacggatggcatgacag\n",
    "taagagaattatgcagtgctgccataaccatgagtgataacactgcggccaacttacttctgacaacgatcggaggaccg\n",
    "aaggagctaaccgcttttttgcacaacatgggggatcatgtaactcgccttgatcgttgggaaccggagctgaatgaagc\n",
    "cataccaaacgacgagcgtgacaccacgatgcctgtagcaatggcaacaacgttgcgcaaactattaactggcgaactac\n",
    "ttactctagcttcccggcaacaattaatagactggatggaggcggataaagttgcaggaccacttctgcgctcggccctt\n",
    "ccggctggctggtttattgctgataaatctggagccggtgagcgtgggtctcgcggtatcattgcagcactggggccaga\n",
    "tggtaagccctcccgtatcgtagttatctacacgacggggagtcaggcaactatggatgaacgaaatagacagatcgctg\n",
    "agataggtgcctcactgattaagcattggtaactgtcagaccaagtttactcatatatactttagattgatttaaaactt\n",
    "catttttaatttaaaaggatctaggtgaagatcctttttgataatctcatgaccaaaatcccttaacgtgagttttcgtt\n",
    "ccactgagcgtcagaccccgtagaaaagatcaaaggatcttcttgagatcctttttttctgcgcgtaatctgctgcttgc\n",
    "aaacaaaaaaaccaccgctaccagcggtggtttgtttgccggatcaagagctaccaactctttttccgaaggtaactggc\n",
    "ttcagcagagcgcagataccaaatactgtccttctagtgtagccgtagttaggccaccacttcaagaactctgtagcacc\n",
    "gcctacatacctcgctctgctaatcctgttaccagtggctgctgccagtggcgataagtcgtgtcttaccgggttggact\n",
    "caagacgatagttaccggataaggcgcagcggtcgggctgaacggggggttcgtgcacacagcccagcttggagcgaacg\n",
    "acctacaccgaactgagatacctacagcgtgagctatgagaaagcgccacgcttcccgaagggagaaaggcggacaggta\n",
    "tccggtaagcggcagggtcggaacaggagagcgcacgagggagcttccagggggaaacgcctggtatctttatagtcctg\n",
    "tcgggtttcgccacctctgacttgagcgtcgatttttgtgatgctcgtcaggggggcggagcctatggaaaaacgccagc\n",
    "aacgcggcctttttacggttcctggccttttgctggccttttgctcacatgttctttcctgcgttatcccctgattctgt\n",
    "ggataaccgtattaccgcctttgagtgagctgataccgctcgccgcagccgaacgaccgagcgcagcgagtcagtgagcg\n",
    "aggaagcggaagagcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacagg\n",
    "tttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttaca\n",
    "ctttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacaggaaacagctatgaccatgatt\n",
    "acgccaagcgcgcaattaaccctcactaaagggaacaaaagctggagctgcaagcttaatgtagtcttatgcaatactct\n",
    "tgtagtcttgcaacatggtaacgatgagttagcaacatgccttacaaggagagaaaaagcaccgtgcatgccgattggtg\n",
    "gaagtaaggtggtacgatcgtgccttattaggaaggcaacagacgggtctgacatggattggacgaaccactgaattgcc\n",
    "gcattgcagagatattgtatttaagtgcctagctcgatacaataaacgggtctctctggttagaccagatctgagcctgg\n",
    "gagctctctggctaactagggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccg\n",
    "tctgttgtgtgactctggtaactagagatccctcagacccttttagtcagtgtggaaaatctctagcagtggcgcccgaa\n",
    "cagggacctgaaagcgaaagggaaaccagagctctctcgacgcaggactcggcttgctgaagcgcgcacggcaagaggcg\n",
    "aggggcggcgactggtgagtacgccaaaaattttgactagcggaggctagaaggagagagatgggtgcgagagcgtcagt\n",
    "attaagcgggggagaattagatcgcgatgggaaaaaattcggttaaggccagggggaaagaaaaaatataaattaaaaca\n",
    "tatagtatgggcaagcagggagctagaacgattcgcagttaatcctggcctgttagaaacatcagaaggctgtagacaaa\n",
    "tactgggacagctacaaccatcccttcagacaggatcagaagaacttagatcattatataatacagtagcaaccctctat\n",
    "tgtgtgcatcaaaggatagagataaaagacaccaaggaagctttagacaagatagaggaagagcaaaacaaaagtaagac\n",
    "caccgcacagcaagcggccgctgatcttcagacctggaggaggagatatgagggacaattggagaagtgaattatataaa\n",
    "tataaagtagtaaaaattgaaccattaggagtagcacccaccaaggcaaagagaagagtggtgcagagagaaaaaagagc\n",
    "agtgggaataggagctttgttccttgggttcttgggagcagcaggaagcactatgggcgcagcctcaatgacgctgacgg\n",
    "tacaggccagacaattattgtctggtatagtgcagcagcagaacaatttgctgagggctattgaggcgcaacagcatctg\n",
    "ttgcaactcacagtctggggcatcaagcagctccaggcaagaatcctggctgtggaaagatacctaaaggatcaacagct\n",
    "cctggggatttggggttgctctggaaaactcatttgcaccactgctgtgccttggaatgctagttggagtaataaatctc\n",
    "tggaacagattggaatcacacgacctggatggagtgggacagagaaattaacaattacacaagcttaatacactccttaa\n",
    "ttgaagaatcgcaaaaccagcaagaaaagaatgaacaagaattattggaattagataaatgggcaagtttgtggaattgg\n",
    "tttaacataacaaattggctgtggtatataaaattattcataatgatagtaggaggcttggtaggtttaagaatagtttt\n",
    "tgctgtactttctatagtgaatagagttaggcagggatattcaccattatcgtttcagacccacctcccaaccccgaggg\n",
    "gacccgacaggcccgaaggaatagaagaagaaggtggagagagagacagagacagatccattcgattagtgaacggatct\n",
    "cgacggttaacttttaaaagaaaaggggggattggggggtacagtgcaggggaaagaatagtagacataatagcaacaga\n",
    "catacaaactaaagaattacaaaaacaaattacaaaaattcaaaattttatcgataagcttgggagttccgcgttacata\n",
    "acttacggtaaatggcccgcctggctgaccgcccaacgacccccgcccattgacgtcaataatgacgtatgttcccatag\n",
    "taacgccaatagggactttccattgacgtcaatgggtggagtatttacggtaaactgcccacttggcagtacatcaagtg\n",
    "tatcatatgccaagtacgccccctattgacgtcaatgacggtaaatggcccgcctggcattatgcccagtacatgacctt\n",
    "atgggactttcctacttggcagtacatctacgtattagtcatcgctattaccatggtgatgcggttttggcagtacatca\n",
    "atgggcgtggatagcggtttgactcacggggatttccaagtctccaccccattgacgtcaatgggagtttgttttggcac\n",
    "caaaatcaacgggactttccaaaatgtcgtaacaactccgccccattgacgcaaatgggcggtaggcgtgtacggtggga\n",
    "ggtctatataagcagagctcgtttagtgaaccgtcagatcgcctggagacgccatccacgctgttttgacctccatagaa\n",
    "gacaccgactctagAGCCACCATGTACCCATACGATGTTCCAGATTACGCTGTGCTTGTGGGCACGCAGGATGTACCCAT\n",
    "ACGATGTTCCAGATTACGCTGTGCTTGTGGGCACGCAGGATGCCATCAGCGCTGCGAATCCCCGGGTTATCGACGACAGC\n",
    "AGAGCCCGCAAGCTCTCCACAGATCTGAAGCGGTGCACCTACTATGAGACGTGCGCGACCTACGGGCTCAATGTGGAGCG\n",
    "TGTCTTCCAGGACGTGGCCCAGAAGGTAGTGGCCTTGCGAAAGAAGCAGCAACTGGCCATCGGGCCCTGCAAGTCACTGC\n",
    "CCAACTCGCCCAGCCACTCGGCCGTGTCCGCCGCCTCCATCCCGGCCGTGCACATCAACCAGGCCACGAATGGCGGCGGC\n",
    "AGCGCCTTCAGCGACTACTCGTCCTCAGTCCCCTCCACCCCCAGCATCAGCCAGCGGGAGCTGCGCATCGAGACCATCGC\n",
    "TGCCTCCTCCACCCCCACACCCATCCGAAAGCAGTCCAAGCGGCGCTCCAACATCTTCACGGACTTGATTAGAGACCAAG\n",
    "GATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCTACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTG\n",
    "AAAGCCTTACAGAAATCTCCAGGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAAC\n",
    "ACTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGACAAAGAATTGGATCTGGAT\n",
    "CATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTGGCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAG\n",
    "CAGTTACAAGCCTTCAAAAATGAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTC\n",
    "CACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCATCTCCATATCATTGAGACCA\n",
    "AATTTGAGATGATCAAACTTATAGATATTGCACGACAGACTGCACAGGGCATGGATTACTTACACGCCAAGTCAATCATC\n",
    "CACAGAGACCTCAAGAGTAATAATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGT\n",
    "GAAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGCACCAGAAGTCATCAGAA\n",
    "TGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATATGCATTTGGGATTGTTCTGTATGAATTGATGACTGGACAG\n",
    "TTACCTTATTCAAACATCAACAACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAA\n",
    "GGTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAAAGAGATGAGAGACCACTCT\n",
    "TTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCATTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTG\n",
    "AATCGGGCTGGTTTCCAAACAGAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATA\n",
    "TGGTGCGTTTCCTGTCCACTGAGtcgacaatcaacctctggattacaaaatttgtgaaagattgactggtattcttaact\n",
    "atgttgctccttttacgctatgtggatacgctgctttaatgcctttgtatcatgctattgcttcccgtatggctttcatt\n",
    "ttctcctccttgtataaatcctggttgctgtctctttatgaggagttgtggcccgttgtcaggcaacgtggcgtggtgtg\n",
    "cactgtgtttgctgacgcaacccccactggttggggcattgccaccacctgtcagctcctttccgggactttcgctttcc\n",
    "ccctccctattgccacggcggaactcatcgccgcctgccttgcccgctgctggacaggggctcggctgttgggcactgac\n",
    "aattccgtggtgttgtcggggaagctgacgtcctttccatggctgctcgcctgtgttgccacctggattctgcgcgggac\n",
    "gtccttctgctacgtcccttcggccctcaatccagcggaccttccttcccgcggcctgctgccggctctgcggcctcttc\n",
    "cgcgtcttcgccttcgccctcagacgagtcggatctccctttgggccgcctccccgcctgGAATTCTACCGGGTAGGGGA\n",
    "GGCGCTTTTCCCAAGGCAGTCTGGAGCATGCGCTTTAGCAGCCCCGCTGGGCACTTGGCGCTACACAAGTGGCCTCTGGC\n",
    "CTCGCACACATTCCACATCCACCGGTAGGCGCCAACCGGCTCCGTTCTTTGGTGGCCCCTTCGCGCCACCTTCTACTCCT\n",
    "CCCCTAGTCAGGAAGTTCCCCCCCGCCCCGCAGCTCGCGTCGTGCAGGACGTGACAAATGGAAGTAGCACGTCTCACTAG\n",
    "TCTCGTGCAGATGGACAGCACCGCTGAGCAATGGAAGCGGGTAGGCCTTTGGGGCAGCGGCCAATAGCAGCTTTGCTCCT\n",
    "TCGCTTTCTGGGCTCAGAGGCTGGGAAGGGGTGGGTCCGGGGGCGGGCTCAGGGGCGGGCTCAGGGGCGGGGCGGGCGCC\n",
    "CGAAGGTCCTCCGGAGGCCCGGCATTCTGCACGCTTCAAAAGCGCACGTCTGCCGCGCTGTTCTCCTCTTCCTCATCTCC\n",
    "GGGCCTTTCGACCTGCAGCCCAAGCTTACCATGACCGAGTACAAGCCCACGGTGCGCCTCGCCACCCGCGACGACGTCCC\n",
    "CAGGGCCGTACGCACCCTCGCCGCCGCGTTCGCCGACTACCCCGCCACGCGCCACACCGTCGATCCGGACCGCCACATCG\n",
    "AGCGGGTCACCGAGCTGCAAGAACTCTTCCTCACGCGCGTCGGGCTCGACATCGGCAAGGTGTGGGTCGCGGACGACGGC\n",
    "GCCGCGGTGGCGGTCTGGACCACGCCGGAGAGCGTCGAAGCGGGGGCGGTGTTCGCCGAGATCGGCCCGCGCATGGCCGA\n",
    "GTTGAGCGGTTCCCGGCTGGCCGCGCAGCAACAGATGGAAGGCCTCCTGGCGCCGCACCGGCCCAAGGAGCCCGCGTGGT\n",
    "TCCTGGCCACCGTCGGCGTCTCGCCCGACCACCAGGGCAAGGGTCTGGGCAGCGCCGTCGTGCTCCCCGGAGTGGAGGCG\n",
    "GCCGAGCGCGCCGGGGTGCCCGCCTTCCTGGAGACCTCCGCGCCCCGCAACCTCCCCTTCTACGAGCGGCTCGGCTTCAC\n",
    "CGTCACCGCCGACGTCGAGGTGCCCGAAGGACCGCGCACCTGGTGCATGACCCGCAAGCCCGGTGCCTGACGCCCGCCCC\n",
    "ACGACCCGCAGCGCCCGACCGAAAGGAGCGCACGACCCCATGCATCTCGAGGGCCCGGTACctttaagaccaatgactta\n",
    "caaggcagctgtagatcttagccactttttaaaagaaaaggggggactggaagggctagctcactcccaacgaagacaag\n",
    "atctgctttttgcttgtactgggtctctctggttagaccagatctgagcctgggagctctctggctgcctagggaaccca\n",
    "ctgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccgtctgttgtgtgactctggtaactagag\n",
    "atccctcagacccttttagtcagtgtggaaaatctctagcagtagtagttcatgtcatcttattattcagtatttataac\n",
    "ttgcaaagaaatgaatatcagagagtgagaggaacttgtttattgcagcttataatggttacaaataaagcaatagcatc\n",
    "acaaatttcacaaataaagcatttttttcactgcattctagttgtggtttgtccaaactcatcaatgtatcttatcatgt\n",
    "ctggctctagctatcccgcccctaactccgcccagttccgcccattctccgccccatggctgactaattttttttattta\n",
    "tgcagaggccgaggccgcctcggcctctgagctattccagaagtagtgaggaggcttttttggaggcctaggcttttgcg\n",
    "tcgagacgtacccaattcgccctatagtgagtcgtattacgcgcgctcactggccgtcgttttacaacgtcgtgactggg\n",
    "aaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgc\n",
    "accgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcgacgcgccctgtagcggcgcattaagcgcggc\n",
    "gggtgtggtggttacgcgcagcgtgaccgctacacttgccagcgccctagcgcccgctcctttcgctttcttcccttcct\n",
    "ttctcgccacgttcgccggctttccccgtcaagctctaaatcgggggctccctttagggttccgatttagtgctttacgg\n",
    "cacctcgaccccaaaaaacttgattagggtgatggttcacgtagtgggccatcgccctgatagacggtttttcgcccttt\n",
    "gacgttggagtccacgttctttaatagtggactcttgttccaaactggaacaacactcaaccctatctcggtctattctt\n",
    "ttgatttataagggattttgccgatttcggcctattggttaaaaaatgagctgatttaacaaaaatttaacgcgaatttt\n",
    "aacaaaatattaacgtttacaatttcc'''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "##Insert your \"Plasmid 2\" sequence\n",
    "\n",
    "p2 = '''\n",
    "caggtggcacttttcggggaaatgtgcgcggaacccctatttgtttatttttctaaatacattcaaatatgtatccgctc\n",
    "atgagacaataaccctgataaatgcttcaataatattgaaaaaggaagagtatgagtattcaacatttccgtgtcgccct\n",
    "tattcccttttttgcggcattttgccttcctgtttttgctcacccagaaacgctggtgaaagtaaaagatgctgaagatc\n",
    "agttgggtgcacgagtgggttacatcgaactggatctcaacagcggtaagatccttgagagttttcgccccgaagaacgt\n",
    "tttccaatgatgagcacttttaaagttctgctatgtggcgcggtattatcccgtattgacgccgggcaagagcaactcgg\n",
    "tcgccgcatacactattctcagaatgacttggttgagtactcaccagtcacagaaaagcatcttacggatggcatgacag\n",
    "taagagaattatgcagtgctgccataaccatgagtgataacactgcggccaacttacttctgacaacgatcggaggaccg\n",
    "aaggagctaaccgcttttttgcacaacatgggggatcatgtaactcgccttgatcgttgggaaccggagctgaatgaagc\n",
    "cataccaaacgacgagcgtgacaccacgatgcctgtagcaatggcaacaacgttgcgcaaactattaactggcgaactac\n",
    "ttactctagcttcccggcaacaattaatagactggatggaggcggataaagttgcaggaccacttctgcgctcggccctt\n",
    "ccggctggctggtttattgctgataaatctggagccggtgagcgtgggtctcgcggtatcattgcagcactggggccaga\n",
    "tggtaagccctcccgtatcgtagttatctacacgacggggagtcaggcaactatggatgaacgaaatagacagatcgctg\n",
    "agataggtgcctcactgattaagcattggtaactgtcagaccaagtttactcatatatactttagattgatttaaaactt\n",
    "catttttaatttaaaaggatctaggtgaagatcctttttgataatctcatgaccaaaatcccttaacgtgagttttcgtt\n",
    "ccactgagcgtcagaccccgtagaaaagatcaaaggatcttcttgagatcctttttttctgcgcgtaatctgctgcttgc\n",
    "aaacaaaaaaaccaccgctaccagcggtggtttgtttgccggatcaagagctaccaactctttttccgaaggtaactggc\n",
    "ttcagcagagcgcagataccaaatactgtccttctagtgtagccgtagttaggccaccacttcaagaactctgtagcacc\n",
    "gcctacatacctcgctctgctaatcctgttaccagtggctgctgccagtggcgataagtcgtgtcttaccgggttggact\n",
    "caagacgatagttaccggataaggcgcagcggtcgggctgaacggggggttcgtgcacacagcccagcttggagcgaacg\n",
    "acctacaccgaactgagatacctacagcgtgagctatgagaaagcgccacgcttcccgaagggagaaaggcggacaggta\n",
    "tccggtaagcggcagggtcggaacaggagagcgcacgagggagcttccagggggaaacgcctggtatctttatagtcctg\n",
    "tcgggtttcgccacctctgacttgagcgtcgatttttgtgatgctcgtcaggggggcggagcctatggaaaaacgccagc\n",
    "aacgcggcctttttacggttcctggccttttgctggccttttgctcacatgttctttcctgcgttatcccctgattctgt\n",
    "ggataaccgtattaccgcctttgagtgagctgataccgctcgccgcagccgaacgaccgagcgcagcgagtcagtgagcg\n",
    "aggaagcggaagagcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacagg\n",
    "tttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttaca\n",
    "ctttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacaggaaacagctatgaccatgatt\n",
    "acgccaagcgcgcaattaaccctcactaaagggaacaaaagctggagctgcaagcttaatgtagtcttatgcaatactct\n",
    "tgtagtcttgcaacatggtaacgatgagttagcaacatgccttacaaggagagaaaaagcaccgtgcatgccgattggtg\n",
    "gaagtaaggtggtacgatcgtgccttattaggaaggcaacagacgggtctgacatggattggacgaaccactgaattgcc\n",
    "gcattgcagagatattgtatttaagtgcctagctcgatacaataaacgggtctctctggttagaccagatctgagcctgg\n",
    "gagctctctggctaactagggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccg\n",
    "tctgttgtgtgactctggtaactagagatccctcagacccttttagtcagtgtggaaaatctctagcagtggcgcccgaa\n",
    "cagggacctgaaagcgaaagggaaaccagagctctctcgacgcaggactcggcttgctgaagcgcgcacggcaagaggcg\n",
    "aggggcggcgactggtgagtacgccaaaaattttgactagcggaggctagaaggagagagatgggtgcgagagcgtcagt\n",
    "attaagcgggggagaattagatcgcgatgggaaaaaattcggttaaggccagggggaaagaaaaaatataaattaaaaca\n",
    "tatagtatgggcaagcagggagctagaacgattcgcagttaatcctggcctgttagaaacatcagaaggctgtagacaaa\n",
    "tactgggacagctacaaccatcccttcagacaggatcagaagaacttagatcattatataatacagtagcaaccctctat\n",
    "tgtgtgcatcaaaggatagagataaaagacaccaaggaagctttagacaagatagaggaagagcaaaacaaaagtaagac\n",
    "caccgcacagcaagcggccgctgatcttcagacctggaggaggagatatgagggacaattggagaagtgaattatataaa\n",
    "tataaagtagtaaaaattgaaccattaggagtagcacccaccaaggcaaagagaagagtggtgcagagagaaaaaagagc\n",
    "agtgggaataggagctttgttccttgggttcttgggagcagcaggaagcactatgggcgcagcctcaatgacgctgacgg\n",
    "tacaggccagacaattattgtctggtatagtgcagcagcagaacaatttgctgagggctattgaggcgcaacagcatctg\n",
    "ttgcaactcacagtctggggcatcaagcagctccaggcaagaatcctggctgtggaaagatacctaaaggatcaacagct\n",
    "cctggggatttggggttgctctggaaaactcatttgcaccactgctgtgccttggaatgctagttggagtaataaatctc\n",
    "tggaacagattggaatcacacgacctggatggagtgggacagagaaattaacaattacacaagcttaatacactccttaa\n",
    "ttgaagaatcgcaaaaccagcaagaaaagaatgaacaagaattattggaattagataaatgggcaagtttgtggaattgg\n",
    "tttaacataacaaattggctgtggtatataaaattattcataatgatagtaggaggcttggtaggtttaagaatagtttt\n",
    "tgctgtactttctatagtgaatagagttaggcagggatattcaccattatcgtttcagacccacctcccaaccccgaggg\n",
    "gacccgacaggcccgaaggaatagaagaagaaggtggagagagagacagagacagatccattcgattagtgaacggatct\n",
    "cgacggttaacttttaaaagaaaaggggggattggggggtacagtgcaggggaaagaatagtagacataatagcaacaga\n",
    "catacaaactaaagaattacaaaaacaaattacaaaaattcaaaattttatcgataagcttgggagttccgcgttacata\n",
    "acttacggtaaatggcccgcctggctgaccgcccaacgacccccgcccattgacgtcaataatgacgtatgttcccatag\n",
    "taacgccaatagggactttccattgacgtcaatgggtggagtatttacggtaaactgcccacttggcagtacatcaagtg\n",
    "tatcatatgccaagtacgccccctattgacgtcaatgacggtaaatggcccgcctggcattatgcccagtacatgacctt\n",
    "atgggactttcctacttggcagtacatctacgtattagtcatcgctattaccatggtgatgcggttttggcagtacatca\n",
    "atgggcgtggatagcggtttgactcacggggatttccaagtctccaccccattgacgtcaatgggagtttgttttggcac\n",
    "caaaatcaacgggactttccaaaatgtcgtaacaactccgccccattgacgcaaatgggcggtaggcgtgtacggtggga\n",
    "ggtctatataagcagagctcgtttagtgaaccgtcagatcgcctggagacgccatccacgctgttttgacctccatagaa\n",
    "gacaccgactctagaggatccaccggtcgccaccatggtgagcaagggcgaggagctgttcaccggggtggtgcccatcc\n",
    "tggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagggcgagggcgatgccacctacggcaag\n",
    "ctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccctgacctacggcgt\n",
    "gcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccagg\n",
    "agcgcaccatcttcttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaac\n",
    "cgcatcgagctgaagggcatcgacttcaaggaggacggcaacatcctggggcacaagctggagtacaactacaacagcca\n",
    "caacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaagatccgccacaacatcgaggacggca\n",
    "gcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctg\n",
    "agcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgg\n",
    "gatcactctcggcatggacgagctgtacaagtaaagcggccgcgtcgacaatcaacctctggattacaaaatttgtgaaa\n",
    "gattgactggtattcttaactatgttgctccttttacgctatgtggatacgctgctttaatgcctttgtatcatgctatt\n",
    "gcttcccgtatggctttcattttctcctccttgtataaatcctggttgctgtctctttatgaggagttgtggcccgttgt\n",
    "caggcaacgtggcgtggtgtgcactgtgtttgctgacgcaacccccactggttggggcattgccaccacctgtcagctcc\n",
    "tttccgggactttcgctttccccctccctattgccacggcggaactcatcgccgcctgccttgcccgctgctggacaggg\n",
    "gctcggctgttgggcactgacaattccgtggtgttgtcggggaagctgacgtcctttccatggctgctcgcctgtgttgc\n",
    "cacctggattctgcgcgggacgtccttctgctacgtcccttcggccctcaatccagcggaccttccttcccgcggcctgc\n",
    "tgccggctctgcggcctcttccgcgtcttcgccttcgccctcagacgagtcggatctccctttgggccgcctccccgcct\n",
    "gGAATTCTACCGGGTAGGGGAGGCGCTTTTCCCAAGGCAGTCTGGAGCATGCGCTTTAGCAGCCCCGCTGGGCACTTGGC\n",
    "GCTACACAAGTGGCCTCTGGCCTCGCACACATTCCACATCCACCGGTAGGCGCCAACCGGCTCCGTTCTTTGGTGGCCCC\n",
    "TTCGCGCCACCTTCTACTCCTCCCCTAGTCAGGAAGTTCCCCCCCGCCCCGCAGCTCGCGTCGTGCAGGACGTGACAAAT\n",
    "GGAAGTAGCACGTCTCACTAGTCTCGTGCAGATGGACAGCACCGCTGAGCAATGGAAGCGGGTAGGCCTTTGGGGCAGCG\n",
    "GCCAATAGCAGCTTTGCTCCTTCGCTTTCTGGGCTCAGAGGCTGGGAAGGGGTGGGTCCGGGGGCGGGCTCAGGGGCGGG\n",
    "CTCAGGGGCGGGGCGGGCGCCCGAAGGTCCTCCGGAGGCCCGGCATTCTGCACGCTTCAAAAGCGCACGTCTGCCGCGCT\n",
    "GTTCTCCTCTTCCTCATCTCCGGGCCTTTCGACCTGCAGCCCAAGCTTACCATGACCGAGTACAAGCCCACGGTGCGCCT\n",
    "CGCCACCCGCGACGACGTCCCCAGGGCCGTACGCACCCTCGCCGCCGCGTTCGCCGACTACCCCGCCACGCGCCACACCG\n",
    "TCGATCCGGACCGCCACATCGAGCGGGTCACCGAGCTGCAAGAACTCTTCCTCACGCGCGTCGGGCTCGACATCGGCAAG\n",
    "GTGTGGGTCGCGGACGACGGCGCCGCGGTGGCGGTCTGGACCACGCCGGAGAGCGTCGAAGCGGGGGCGGTGTTCGCCGA\n",
    "GATCGGCCCGCGCATGGCCGAGTTGAGCGGTTCCCGGCTGGCCGCGCAGCAACAGATGGAAGGCCTCCTGGCGCCGCACC\n",
    "GGCCCAAGGAGCCCGCGTGGTTCCTGGCCACCGTCGGCGTCTCGCCCGACCACCAGGGCAAGGGTCTGGGCAGCGCCGTC\n",
    "GTGCTCCCCGGAGTGGAGGCGGCCGAGCGCGCCGGGGTGCCCGCCTTCCTGGAGACCTCCGCGCCCCGCAACCTCCCCTT\n",
    "CTACGAGCGGCTCGGCTTCACCGTCACCGCCGACGTCGAGGTGCCCGAAGGACCGCGCACCTGGTGCATGACCCGCAAGC\n",
    "CCGGTGCCTGACGCCCGCCCCACGACCCGCAGCGCCCGACCGAAAGGAGCGCACGACCCCATGCATCTCGAGGGCCCGGT\n",
    "ACctttaagaccaatgacttacaaggcagctgtagatcttagccactttttaaaagaaaaggggggactggaagggctag\n",
    "ctcactcccaacgaagacaagatctgctttttgcttgtactgggtctctctggttagaccagatctgagcctgggagctc\n",
    "tctggctgcctagggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagtagtgtgtgcccgtctgtt\n",
    "gtgtgactctggtaactagagatccctcagacccttttagtcagtgtggaaaatctctagcagtagtagttcatgtcatc\n",
    "ttattattcagtatttataacttgcaaagaaatgaatatcagagagtgagaggaacttgtttattgcagcttataatggt\n",
    "tacaaataaagcaatagcatcacaaatttcacaaataaagcatttttttcactgcattctagttgtggtttgtccaaact\n",
    "catcaatgtatcttatcatgtctggctctagctatcccgcccctaactccgcccagttccgcccattctccgccccatgg\n",
    "ctgactaattttttttatttatgcagaggccgaggccgcctcggcctctgagctattccagaagtagtgaggaggctttt\n",
    "ttggaggcctaggcttttgcgtcgagacgtacccaattcgccctatagtgagtcgtattacgcgcgctcactggccgtcg\n",
    "ttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctgg\n",
    "cgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcgacgcgccctg\n",
    "tagcggcgcattaagcgcggcgggtgtggtggttacgcgcagcgtgaccgctacacttgccagcgccctagcgcccgctc\n",
    "ctttcgctttcttcccttcctttctcgccacgttcgccggctttccccgtcaagctctaaatcgggggctccctttaggg\n",
    "ttccgatttagtgctttacggcacctcgaccccaaaaaacttgattagggtgatggttcacgtagtgggccatcgccctg\n",
    "atagacggtttttcgccctttgacgttggagtccacgttctttaatagtggactcttgttccaaactggaacaacactca\n",
    "accctatctcggtctattcttttgatttataagggattttgccgatttcggcctattggttaaaaaatgagctgatttaa\n",
    "caaaaatttaacgcgaattttaacaaaatattaacgtttacaatttcc\n",
    "'''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "## List all common restriction enzymes that cut both plasmids exactly N times\n",
    "\n",
    "N = 1 #how many cuts?\n",
    "\n",
    "for e in Restriction.CommOnly: #scan only for commonly-used enzymes\n",
    "    if len(e.search(Seq(p1))) == N:\n",
    "        if len(e.search(Seq(p1))) == N:\n",
    "            print(e)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Find common RE in many sequences\n",
    "from collections import Counter\n",
    "\n",
    "def parse_fasta(text):\n",
    "    '''file_path => dict\n",
    "    Return a dict of id:sequences.\n",
    "    '''\n",
    "    d = {}\n",
    "    _id = False\n",
    "    seq = ''\n",
    "    for line in text.split('\\n'):\n",
    "        if line != '':\n",
    "            if line.startswith('>'):\n",
    "                if not _id:\n",
    "                    _id = line[1:].strip()\n",
    "                elif _id and seq:\n",
    "                    d.update({_id:seq})\n",
    "                    _id = line[1:].strip()\n",
    "                    seq = ''\n",
    "            else:\n",
    "                seq += line.strip()\n",
    "            d.update({_id:seq})\n",
    "    return d\n",
    "\n",
    "\n",
    "text = \\\n",
    "'''\n",
    ">BB200_1 (len:243  mean_flex:13.0  max_flex:14.9  entropy:1.99  GC%:44.86)\n",
    "GGGCATGCACAGATGTACACGGCGGCGCAAGATGATGTGCCGAACCTGACATGGCATCGACTGGTATGGATCAATACTGATGCGATATCGATACCGGATAAATCATATATGCATAATATCACATTATATTAATTATAATACATCGGCGTACATATACACGTACGCATCATTTCACTATCTATCGGTACTATACGTAGTGCCGGTCTGTTGGCCGGGCGACATAGATGCTGCATGACATAGCCC\n",
    "\n",
    ">BB200_2 (len:244  mean_flex:13.15  max_flex:14.69  entropy:1.96  GC%:38.52)\n",
    "GGGCATGCACAGATGTACACGTGACGCAACGATGATGTTAGCTATTTGTTCAATGACAAATCTGGTATGATCAATACCGATGCGATATTGATATCTGATAACTCATATATGTAGAATATCACATTATATTTATTATAATACATCGTCGAACATATACACAATGCATCTTATCTATACGTATCGGGATAGCGTTGGCATAGCACTGGATGGCATGACCCTCATTAGATGCTGCATGACATAGCCC\n",
    "\n",
    ">BB200_3 (len:244  mean_flex:13.06  max_flex:14.9  entropy:1.96  GC%:39.75)\n",
    "GGGCATGCACAGATGTACACGAGACCGCAAGATGATGTTCATTCTTGAACATGAGATCGGATGGGTATGGATCAATACCGATGCGATATGATAACTGATAAATCATATATCTATAATATCACATTATATTAATTATAATACAGGATCGTTACATGCATACACAATGTATACTATACGTATTCGGTAGTTAGTGTACGGTCGGAATGGAGGTGGTGGCGGTGATAGATGCTGCATGACATAGCCC\n",
    "\n",
    ">BB200_4 (len:243  mean_flex:13.29  max_flex:14.44  entropy:1.93  GC%:34.57)\n",
    "GGGCATGCACAGATGTACACGAATCCCGAAGATGTTGTCCATTCATTGAATATGAGATCTCATGGTATGATCAATATCGGATGCGATATTGATACTGATAAATCATATATGCATAATCTCACATTATATTTATTATAATAAATCATCGTAGATATACACAATGTGAATTGTATACAATGGATAGTATAACTATCCAATTTCTTTGAGCATTGGCCTTGGTGTAGATGCTGCATGACATAGCCC\n",
    "\n",
    ">BB200_5 (len:243  mean_flex:13.37  max_flex:14.52  entropy:1.94  GC%:35.8)\n",
    "GGGCATGCACAGATGTACACGAATCCGTGAGATGACTATCTTATTTGTGACATTCATCGATCTGGATATGATCAATACCATGCGATATTGATTACTGATAAATCATATATGTAGAATATCACATTATATTAATTATAATAAATCGTCGTACATATACATCCACAATTAGCTATGTATACTATCTATAGAGATGGTGCATCATCGTACTCCACCATTCCCACTAGATGCTGCATGACATAGCCC\n",
    "'''\n",
    "\n",
    "\n",
    "\n",
    "sequences = parse_fasta(text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "BseXI \t GCAGC\n",
      "PsiI \t TTATAA\n",
      "Cac8I \t GCNNGC\n",
      "BstC8I \t GCNNGC\n",
      "PaeI \t GCATGC\n",
      "Bsp1407I \t TGTACA\n",
      "BstAUI \t TGTACA\n",
      "SphI \t GCATGC\n",
      "TatI \t WGTACW\n",
      "ApeKI \t GCWGC\n",
      "BbvI \t GCAGC\n",
      "Lsp1109I \t GCAGC\n",
      "TseI \t GCWGC\n",
      "BstV1I \t GCAGC\n",
      "AanI \t TTATAA\n",
      "BsrGI \t TGTACA\n"
     ]
    }
   ],
   "source": [
    "N = 1 #how many cuts?\n",
    "\n",
    "c = Counter()\n",
    "for _id, seq in sequences.items():\n",
    "    for e in Restriction.CommOnly:\n",
    "        if len(e.search(Seq(seq))) == N:\n",
    "            c.update({str(e)})\n",
    "\n",
    "            \n",
    "for e in Restriction.CommOnly:\n",
    "    if str(e) in c:\n",
    "        if c[str(e)] == len(sequences):\n",
    "            print(str(e),'\\t', e.site)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'GCATC'"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "e.site"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}