PPR_Maker_v5.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Welcome to the PPR Maker\n",
      "\n",
      "Loading...\n",
      "\n",
      "Done\n",
      "\n",
      "How many PPR proteins do you want to make? 2\n",
      "\n",
      "Please enter binding sequence number 1: uauauauauu\n",
      "\n",
      "Please enter binding sequence number 2: cucucucccaucuaa\n",
      "\n",
      " PPR Plasmids  Plate Well\n",
      "   1    R1-38      1   D2\n",
      "   1    R2-36      1  G12\n",
      "   1    R3-10      2  A10\n",
      "   1    R4-16      2   F4\n",
      "   2    R1-23      1  B11\n",
      "   2    R2-30      1   G6\n",
      "   2    R3-41      2   D5\n",
      "   2    R4-21      2   F9\n",
      "   2    R5-41      3   D5\n",
      "   2    R6-33      3   G9\n",
      "\n",
      "Protocol file has been created\n",
      "\n",
      "Press ENTER to exit\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "''"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# WELCOME\n",
    "\n",
    "# This version of the software does not require additional files. You only need to run this one block of code.\n",
    "\n",
    "print('')\n",
    "print('Welcome to the PPR Maker')\n",
    "print('')\n",
    "print('Loading...')\n",
    "print('')\n",
    "\n",
    "# LIBRARIES\n",
    "\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "import datetime as dt\n",
    "\n",
    "# FUNCTIONS\n",
    "\n",
    "# Integer validation\n",
    "def is_number(s):\n",
    "    try:\n",
    "        float(s)\n",
    "        return True\n",
    "    except ValueError:\n",
    "        pass\n",
    "    try:\n",
    "        import unicodedata\n",
    "        unicodedata.numeric(s)\n",
    "        return True\n",
    "    except (TypeError, ValueError):\n",
    "        pass\n",
    "    return False\n",
    "\n",
    "# Find the coordinates of an item in a 2D list\n",
    "def coordinates(myList, v):\n",
    "    boolean = False\n",
    "    for i, x in enumerate(myList):\n",
    "        if v in x:\n",
    "            boolean = True\n",
    "            return (i, x.index(v))\n",
    "    if boolean == False:\n",
    "        print('Element not in list')\n",
    "\n",
    "# INITIALIZATIONS\n",
    "\n",
    "# RNA bases and PPR motifs\n",
    "RNAbases = ['U','C','A','G']\n",
    "PPRmotifs = ['ND','NS','SN','TD']\n",
    "\n",
    "# All plasmids\n",
    "allPlasmids = []\n",
    "for i in range(0,6):\n",
    "    for j in range(0,48):\n",
    "        allPlasmids.append('R' + str(i+1) + '-' + str(j+1))\n",
    "allPlasmidsX = [allPlasmids[i:i + 12] for i in range(0, len(allPlasmids), 12)]\n",
    "\n",
    "# Block 1 (structuraly identical to blocks 3 and 5)\n",
    "Block1 = [[],[],[],[]]\n",
    "for i in range(0,48):\n",
    "    Block1[0].append(i+1)\n",
    "for i in range(0,12):\n",
    "    Block1[1].append('SN')\n",
    "for i in range(12,24):\n",
    "    Block1[1].append('NS')\n",
    "for i in range(24,36):\n",
    "    Block1[1].append('TD')   \n",
    "for i in range(36,48):\n",
    "    Block1[1].append('ND')\n",
    "for i in range(0,3):\n",
    "    Block1[2].append('SN')\n",
    "for i in range(3,6):\n",
    "    Block1[2].append('NS')\n",
    "for i in range(6,9):\n",
    "    Block1[2].append('TD')\n",
    "for i in range(9,12):\n",
    "    Block1[2].append('ND')\n",
    "for i in range(12,24):\n",
    "    Block1[2].append(Block1[2][i-12])\n",
    "for i in range(24,48):\n",
    "    Block1[2].append(Block1[2][i-24])\n",
    "Block1[3].append('S')\n",
    "Block1[3].append('N')\n",
    "Block1[3].append('T')\n",
    "for i in range(3,48):\n",
    "    Block1[3].append(Block1[3][i-3])\n",
    "Block1X = [[],[]]\n",
    "for i in range(0,48):\n",
    "    Block1X[0].append(Block1[0][i])\n",
    "    Block1X[1].append(Block1[1][i] + Block1[2][i] + Block1[3][i])\n",
    "    \n",
    "# Block 2 (structurally identical to blocks 4 and 6)\n",
    "Block2 = [[],[],[],[]]\n",
    "for i in range(0,48):\n",
    "    Block2[0].append(i+1)\n",
    "for i in range(0,16):\n",
    "    Block2[1].append('N')\n",
    "for i in range(16,32):\n",
    "    Block2[1].append('S')\n",
    "for i in range(32,48):\n",
    "    Block2[1].append('D')\n",
    "for i in range(0,4):\n",
    "    Block2[2].append('SN')\n",
    "for i in range(4,8):\n",
    "    Block2[2].append('NS')\n",
    "for i in range(8,12):\n",
    "    Block2[2].append('TD')\n",
    "for i in range(12,16):\n",
    "    Block2[2].append('ND')\n",
    "for i in range(16,48):\n",
    "    Block2[2].append(Block2[2][i-16])\n",
    "Block2[3].append('SN')\n",
    "Block2[3].append('NS')\n",
    "Block2[3].append('TD')\n",
    "Block2[3].append('ND')\n",
    "for i in range(4,48):\n",
    "    Block2[3].append(Block2[3][i-4])\n",
    "Block2X = [[],[]]\n",
    "for i in range(0,48):\n",
    "    Block2X[0].append(Block2[0][i])\n",
    "    Block2X[1].append(Block2[1][i] + Block2[2][i] + Block2[3][i])\n",
    "\n",
    "print('Done')\n",
    "print('')\n",
    "    \n",
    "howMany = 0\n",
    "while howMany == 0:\n",
    "    howMany = input('How many PPR proteins do you want to make? ')\n",
    "    if is_number(howMany) == True:\n",
    "        if float(howMany) <= 0:\n",
    "            howMany = 0\n",
    "            print('Must be a positive integer')\n",
    "        else:\n",
    "            if (float(howMany)).is_integer() == False:\n",
    "                howMany = 0\n",
    "                print('Must be a positive integer')\n",
    "            else:\n",
    "                howMany = int(howMany)\n",
    "    else:\n",
    "        howMany = 0\n",
    "        print('Must be a positive integer')\n",
    "print('')\n",
    "    \n",
    "finalPlasmids, plates, wells, PPRID = [], [], [], []\n",
    "for k in range(0, howMany):\n",
    "    \n",
    "    # Binding sequence?\n",
    "    bindingSequence = 0\n",
    "    while bindingSequence == 0:\n",
    "        if howMany == 1:\n",
    "            bindingSequence = input('Please enter the binding sequence: ')\n",
    "        else:\n",
    "            bindingSequence = input('Please enter binding sequence number ' + str(k+1) + ': ')\n",
    "        print('')\n",
    "        if bindingSequence == '':\n",
    "            bindingSequence = 0\n",
    "            print('Invalid entry')\n",
    "            print('')\n",
    "        elif len(bindingSequence) != 10 and len(bindingSequence) != 15:\n",
    "            bindingSequence = 0\n",
    "            print('The length of the binding sequence must be either 10 or 15')\n",
    "            print('')\n",
    "        else:\n",
    "            bindingSequenceX = bindingSequence\n",
    "            bindingSequence = bindingSequence.upper()\n",
    "            i = 0\n",
    "            while i in range(0, len(bindingSequenceX)):\n",
    "                if bindingSequence[i] not in {'T','U','C','A','G'}:\n",
    "                    i = len(bindingSequence)\n",
    "                    bindingSequence = 0\n",
    "                    print('Invalid sequence')\n",
    "                    print('')\n",
    "                else:\n",
    "                    i = i + 1\n",
    "    if 'T' in bindingSequence:\n",
    "        bindingSequence = bindingSequence.replace('T','U')\n",
    "            \n",
    "    # Split the binding sequence\n",
    "    bindingSequenceX = ''\n",
    "    for i in range(0, len(bindingSequence)):\n",
    "        if i == len(bindingSequence) - 1:\n",
    "            bindingSequenceX = bindingSequenceX + bindingSequence[i]\n",
    "        else:\n",
    "            bindingSequenceX = bindingSequenceX + bindingSequence[i] + '.'\n",
    "    listBindingSequence = bindingSequenceX.split('.')\n",
    "        \n",
    "    # Build the PPR\n",
    "    i, j, PPR = 0, 0, ''\n",
    "    while i <= len(bindingSequence) - 1:\n",
    "        if bindingSequence[i] == RNAbases[j]:\n",
    "            if i == 0:\n",
    "                PPR = PPRmotifs[j]\n",
    "                i = i + 1\n",
    "                j = 0\n",
    "            else:\n",
    "                PPR = PPR + ' ' + PPRmotifs[j]\n",
    "                i = i + 1\n",
    "                j = 0\n",
    "        else:\n",
    "            j = j + 1\n",
    "    listPPR = PPR.split()\n",
    "        \n",
    "    # Divide listPPR in 2.5mers\n",
    "    PPRStr = ''\n",
    "    counter = 0\n",
    "    for i in range(0,len(listPPR)):\n",
    "        for j in range(0,2):\n",
    "            if counter < 5:\n",
    "                PPRStr = PPRStr + listPPR[i][j]\n",
    "                counter = counter + 1\n",
    "            else:\n",
    "                PPRStr = PPRStr + '.' + listPPR[i][j]\n",
    "                counter = 1\n",
    "    PPRStr = PPRStr.split('.')\n",
    "        \n",
    "    # Plasmids\n",
    "    plasmids = []\n",
    "    if len(bindingSequence) == 5:\n",
    "        plasmids.append(Block1X[0][Block1X[1].index(PPRStr[0])])\n",
    "        plasmids.append(Block2X[0][Block2X[1].index(PPRStr[1])])\n",
    "    elif len(bindingSequence) == 10:\n",
    "        plasmids.append(Block1X[0][Block1X[1].index(PPRStr[0])])\n",
    "        plasmids.append(Block2X[0][Block2X[1].index(PPRStr[1])])\n",
    "        plasmids.append(Block1X[0][Block1X[1].index(PPRStr[2])])\n",
    "        plasmids.append(Block2X[0][Block2X[1].index(PPRStr[3])])\n",
    "    elif len(bindingSequence) == 15:\n",
    "        plasmids.append(Block1X[0][Block1X[1].index(PPRStr[0])])\n",
    "        plasmids.append(Block2X[0][Block2X[1].index(PPRStr[1])])\n",
    "        plasmids.append(Block1X[0][Block1X[1].index(PPRStr[2])])\n",
    "        plasmids.append(Block2X[0][Block2X[1].index(PPRStr[3])])\n",
    "        plasmids.append(Block1X[0][Block1X[1].index(PPRStr[4])])\n",
    "        plasmids.append(Block2X[0][Block2X[1].index(PPRStr[5])])\n",
    "    plasmidsLen = len(plasmids)\n",
    "    for i in range(0,plasmidsLen):\n",
    "        finalPlasmids.append('R' + str(i+1) + '-' + str(plasmids[i]))\n",
    "            \n",
    "    # Plates\n",
    "    plates += 2 * [1]\n",
    "    if plasmidsLen == 4:\n",
    "        plates += 2 * [2]\n",
    "    if plasmidsLen == 6:\n",
    "        plates += 2 * [2]\n",
    "        plates += 2 * [3]\n",
    "        \n",
    "    # Wells\n",
    "    for i in range(0,plasmidsLen):\n",
    "        x, y = coordinates(allPlasmidsX,finalPlasmids[i+len(PPRID)])[0], coordinates(allPlasmidsX,finalPlasmids[i+len(PPRID)])[1]\n",
    "        if x == 0 or x == 8 or x == 16:\n",
    "            wells.append('A' + str(y+1))\n",
    "        if x == 1 or x == 9 or x == 17:\n",
    "            wells.append('B' + str(y+1))\n",
    "        if x == 2 or x == 10 or x == 18:\n",
    "            wells.append('C' + str(y+1))\n",
    "        if x == 3 or x == 11 or x == 19:\n",
    "            wells.append('D' + str(y+1))\n",
    "        if x == 4 or x == 12 or x == 20:\n",
    "            wells.append('E' + str(y+1))\n",
    "        if x == 5 or x == 13 or x == 21:\n",
    "            wells.append('F' + str(y+1))\n",
    "        if x == 6 or x == 14 or x == 22:\n",
    "            wells.append('G' + str(y+1))\n",
    "        if x == 7 or x == 15 or x == 23:\n",
    "            wells.append('H' + str(y+1))\n",
    "        \n",
    "    for i in range(0, plasmidsLen):\n",
    "        PPRID.append(k+1)\n",
    "        \n",
    "# Display results\n",
    "df = pd.DataFrame({\n",
    "    'PPR':PPRID,\n",
    "    'Plasmids':finalPlasmids,\n",
    "    'Plate':plates,\n",
    "    'Well':wells})\n",
    "print(df.to_string(index = False))\n",
    "print('')\n",
    "\n",
    "# -----------------------\n",
    "# OT-2 protocol generator\n",
    "# -----------------------\n",
    "\n",
    "# Extract experiment variables from dataframe\n",
    "numPPR = df['PPR'].iloc[-1]\n",
    "\n",
    "# Map PPR output wells\n",
    "outwells = []\n",
    "for i in ['E','F','G','H']:\n",
    "    for j in range(12):\n",
    "        outwells.append(i + str(j+1))\n",
    "\n",
    "head = \"\"\"# HEAD\n",
    "\n",
    "from opentrons import protocol_api\n",
    "\n",
    "# Experiment metadata\n",
    "metadata = {'protocolName': 'FusR',\n",
    "    'author': 'SRC & GMG',\n",
    "    'description': 'This script results in the assembly of PPR proteins.',\n",
    "    'apiLevel': '2.8'}\n",
    "\n",
    "# OT labware\n",
    "def run(protocol: protocol_api.ProtocolContext):\n",
    "    # Labware\n",
    "    R1 = protocol.load_labware('nest_96_wellplate_100ul_pcr_full_skirt', 4)\n",
    "    R2 = protocol.load_labware('nest_96_wellplate_100ul_pcr_full_skirt', 5)\n",
    "    R3 = protocol.load_labware('nest_96_wellplate_100ul_pcr_full_skirt', 6)\n",
    "    MISC = protocol.load_labware('nest_96_wellplate_100ul_pcr_full_skirt', 2)\n",
    "    tiprack_1 = protocol.load_labware('geb_96_tiprack_10ul', 1)\n",
    "    tiprack_2 = protocol.load_labware('geb_96_tiprack_10ul', 3)\n",
    "    tiprack_3 = protocol.load_labware('geb_96_tiprack_10ul', 7)\n",
    "    tiprack_4 = protocol.load_labware('geb_96_tiprack_10ul', 8)\n",
    "    # Pipettes\n",
    "    p20 = protocol.load_instrument(\n",
    "        'p20_single_gen2', 'right', tip_racks=\n",
    "        [tiprack_1, tiprack_2, tiprack_3, tiprack_4])\n",
    "\n",
    "# COMMANDS\n",
    "\"\"\"\n",
    "\n",
    "commands = \"\"\"p20.transfer(1, R1['WELL1'], MISC['OUT'])\n",
    "p20.transfer(1, R1['WELL2'], MISC['OUT'])\n",
    "p20.transfer(1, R2['WELL3'], MISC['OUT'])\n",
    "p20.transfer(1, R2['WELL4'], MISC['OUT'])\n",
    "flag10mer = True\n",
    "if flag10mer:\n",
    "    p20.transfer(1, MISC['A1'], MISC['OUT']) # Backbone\n",
    "    p20.transfer(1, MISC['A2'], MISC['OUT']) # Buffer\n",
    "    p20.transfer(3.25, MISC['A3'], MISC['OUT']) # Water\n",
    "else:\n",
    "    p20.transfer(1, R3['WELL5'], MISC['OUT'])\n",
    "    p20.transfer(1, R3['WELL6'], MISC['OUT'])\n",
    "    p20.transfer(1, MISC['A1'], MISC['OUT']) # Backbone\n",
    "    p20.transfer(1, MISC['A2'], MISC['OUT']) # Buffer\n",
    "    p20.transfer(1.25, MISC['A3'], MISC['OUT']) # Water\n",
    "\"\"\"\n",
    "\n",
    "# Generate protocol\n",
    "for i in range(numPPR):\n",
    "    \n",
    "    # Select subset of PPR info from df\n",
    "    dfPPR = df[df['PPR'] == i+1]\n",
    "    \n",
    "    # Change flag10PPR to false if assembling a 15nt-targeting PPR\n",
    "    if len(dfPPR.index) == 6:\n",
    "        commands = commands.replace('True', 'False')\n",
    "    \n",
    "    # Add commands to head for each PPR    \n",
    "    head += '\\n'\n",
    "    head += commands\n",
    "            \n",
    "    # Replace tags in commands with info on dfPPR\n",
    "    for j in range(len(dfPPR.index)) :\n",
    "        head = head.replace('WELL' + str(j+1), dfPPR['Well'].iloc[j])\n",
    "        head = head.replace('OUT', outwells[i])\n",
    "    \n",
    "    # Generate output file with timestamp\n",
    "    with open(dt.datetime.now().strftime('%Y-%m-%d_%H.%M.%S') + '_OTprotocol.py', 'w') as txt:\n",
    "        txt.write(head)\n",
    "   \n",
    "print('Protocol file has been created')\n",
    "print('')\n",
    "input('Press ENTER to exit')"
   ]
  },
  {
   "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": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}