Sequencing_Primers.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import  re\n",
    "from Bio.SeqUtils import MeltingTemp as mt\n",
    "from Bio.Seq import Seq\n",
    "from Bio.SeqUtils.MeltingTemp import make_table, DNA_NN2\n",
    "import pyperclip\n",
    "#https://biopython.org/docs/1.75/api/Bio.SeqUtils.MeltingTemp.html\n",
    "Breslauer= mt.DNA_NN1\n",
    "Santalucia= mt.DNA_NN4 #same as benchling\n",
    "Tm_Opt =Santalucia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def reverse_complement(Seq):\n",
    "    Rv=''\n",
    "    for bp in Seq.upper():\n",
    "        if bp == 'A':\n",
    "            Rv+='T'\n",
    "        if bp == 'T' or bp == 'U':\n",
    "            Rv+='A'\n",
    "        if bp == 'C':\n",
    "            Rv+='G'\n",
    "        if bp == 'G':\n",
    "            Rv+='C'\n",
    "    assert len(Rv)==len(Seq), \"There was an error reversing, Check Input Sequence\"\n",
    "    return Rv[::-1]\n",
    "\n",
    "def Anneal2Patch(Patch, Reverse):\n",
    "    Patch=Patch.upper()\n",
    "    if Reverse == True:\n",
    "        Patch = reverse_complement(Patch)\n",
    "        \n",
    "    GC_clamps=re.finditer(\"[G|C][G|C]\",Patch[20:])\n",
    "\n",
    "    for clamp in GC_clamps:\n",
    "        found=0\n",
    "        #3' of primer\n",
    "        ThreeP = clamp.span()[1]+20 #position on patch\n",
    "        for bp in [0,+1,-1,+2,-2]: #allows the primer length to vary a little\n",
    "            FiveP = ThreeP  - 20 + bp\n",
    "\n",
    "            Anneal=Patch[FiveP:ThreeP] #primer binding site\n",
    "\n",
    "            #find if Annealing region has AT region of 3bp or more\n",
    "            #the following will detect: streches of A or T of length 3+\n",
    "            #AT region of length 5+\n",
    "            ATs=re.findall(\"AAA+|TTT+|[A/T][A/T][A/T][A/T][A/T]+\",Anneal) #[A/T][A/T][A/T]+\n",
    "    \n",
    "            \n",
    "            Tm=mt.Tm_NN( Anneal , nn_table=Tm_Opt, check=False)\n",
    "            \n",
    "            if 48 <Tm and Tm< 54 and len(ATs)==0:\n",
    "                #print(Anneal,ThreeP)\n",
    "                #here we return the primers left most position on the patch \n",
    "                return Anneal, ThreeP if Reverse == False else len(Patch) - ThreeP \n",
    "    return None, None\n",
    "\n",
    "\n",
    "\n",
    "def design_sequencing_primers(Seq):\n",
    "    print('Has len', len(Seq))\n",
    "\n",
    "    Primers_List={}\n",
    "    patch=Seq[0:200]\n",
    "    primer_num=1\n",
    "    Primer_Fwd, Patch_Pos= Anneal2Patch(patch, Reverse=False)\n",
    "    Primers_List['Primer'+str(primer_num)] = Primer_Fwd\n",
    "    primer_num+=1\n",
    "\n",
    "    Current_pos= Patch_Pos #right most limit of any most right primer\n",
    "\n",
    "    while len(Seq) - Current_pos > 1300: #the bckwd primer on XII-5 down can cover 300bp of insert\n",
    "\n",
    "      #  print('Current_pos start',Current_pos)\n",
    "\n",
    "        Primer_Bwd = None\n",
    "        down=0 #used to enlarge search area\n",
    "        #this while loop expands search area to the left by 50bp if a backwd primer cant be found\n",
    "        while Primer_Bwd == None:\n",
    "            #patch_up: patch upper limit\n",
    "            patch_up=min(Current_pos + 1900 , len(Seq) ) #avoids going beyond seq length\n",
    "            patch_down= patch_up-150-down\n",
    "            patch_Bwd=Seq[ patch_down:patch_up] #landing area for back primer\n",
    "            Primer_Bwd, Primer_Pos = Anneal2Patch(patch_Bwd, Reverse=True) #finds bckd primer\n",
    "            down+=50\n",
    "        Primers_List['Primer'+str(primer_num)] = Primer_Bwd\n",
    "        primer_num+=1\n",
    "\n",
    "        Current_pos = patch_down + Primer_Pos \n",
    "       # print('Current_pos after back',Current_pos, patch_up,patch_down )\n",
    "        #tries to find primer in the 50 bp immediately before the 200bp buffer region\n",
    "         #if primer is not found tries to go down an extra 50bp:\n",
    "        Primer_Fwd = None\n",
    "        down=50\n",
    "        while Primer_Fwd == None:\n",
    "\n",
    "            patch_up = Current_pos-200\n",
    "            patch_down = patch_up - down\n",
    "            patch_Fwd=Seq[ patch_down: patch_up] #landing area for forward primer\n",
    "            Primer_Fwd, Primer_pos = Anneal2Patch(patch_Fwd, Reverse=False)\n",
    "            down+=50\n",
    "        Primers_List['Primer'+str(primer_num)] =Primer_Fwd\n",
    "        primer_num+=1\n",
    "\n",
    "\n",
    "        Current_pos = patch_down + Primer_pos  \n",
    "      #  print('Current_pos after front',Current_pos)\n",
    "        print('... Done' )\n",
    "        \n",
    "    return Primers_List\n",
    "    \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Imput your DNA sequence to be sequenced"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "#when sequencing a user integration plasmid, copy from homology up, to the end of your insert\n",
    "#this script will always find the same 1st fwd primer (tgagtcaagttaggtcatcc) \n",
    "#you can also always use the last reverse primer ()\n",
    "Sequences={}\n",
    "Sequences['insert_pCCM001']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtGATCCAGGCAACTTTAGTGCtgacacataatactccataggtattttattatacaaataatgtgtttgaacttattaaaacattcttttaaggtataaacaacaggcatatatatatgtgtgcgacgacacatgatcatatggcatgcatgtgctctgtatgtatataaaactcttgttttcttcttttctctaaatattctttccttatacattaggacctttgcagcataaattactatacttctatagacacacaaacacaaatacacacactaaattaataatctgtcataaaacaatgtctaaaggtgaagaattattcactggtgttgtcccaattttggttgaattagatggtgatgttaatggtcacaaattttctgtctccggtgaaggtgaaggtgatgctacttacggtaaattgaccttaaaatttatttgtactactggtaaattgccagttccatggccaaccttagtcactactttcggttatggtgttcaatgttttgcgagatacccagatcatatgaaacaacatgactttttcaagtctgccatgccagaaggttatgttcaagaaagaactatttttttcaaagatgacggtaactacaagaccagagctgaagtcaagtttgaaggtgataccttagttaatagaatcgaattaaaaggtattgattttaaagaagatggtaacattttaggtcacaaattggaatacaactataactctcacaatgtttacatcatggctgacaaacaaaagaatggtatcaaagttaacttcaaaattagacacaacattgaagatggttctgttcaattagctgaccattatcaacaaaatactccaattggtgatggtccagtcttgttaccagacaaccattacttatccactcaatctgccttatccaaagatccaaacgaaaagagagaccacatggtcttgttagaatttgttactgctgctggtattacccatggtatggatgaattgtacaaataaatcgcgtgcattcatccgctctaaccgaaaaggaaggagttagacaacctgaagtctaggtccctatttatttttttatagttatgttagtattaagaacgttatttatatttcaaatttttcttttttttctgtacagacgcgtgtacgcatgtaacattatactgaaaaccttgcttgagaaggttttgggacgctcgaAGATCGCGTCAGCTGAAatcgcgtgcattc'\n",
    "Sequences['insert_pCCM002']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtAGCGGATAACAATTTCACACAggaaacagctatgaccatgattacgccaagcgcgcaattaaccctcactaaagggaacaaaagctggagctcttcttaggcacaacaatatttataaaagaagaatgtaagtatgacgacgaaaacgaaaagactaatagtttcatataatactaaacgatttcaattttcgttttatatccttcctattcataaattttatttcgctatgccaataatgagtggatgtatagttgatatctgtttcgataattttaaagtagatagtaaaatcttactgacatgaataatccgtccaaaactagattactgtatacaagcatatttaaaaaaataatgaaactatgatcaaaaaactgtgctactacagcggtgttgttatccgatacaaccggatatttttcttttaatgagtctaaaccgtgatagcttcaggttaatacaatcaaaaaaagctcaaatattcttttaatgccgcgttcacagattccaattgaatacaactaggtagttcattatatgaagcctttgctactatttttcactatagtctgccttcaccttaatgcagacatccacatattttaatcactttaaaataaaaaggaagatatattagaagctatgatccaatctgtaagccagattaaaattcacgaactcttctttcatttgaattgaatgctttgagttggggtagattatcgcaaattactcatcacatttattgactacgaacttgctgatgtcctttttttatttatatttttcttcagtgaagcgattttttttttacacagaccaagacggaaaaaagtagctaaggaagaaaacaaaatcatgaaaaaaatgtgaagtgatcatgcacatcgcatcaacttaaacattggcttagagatatatagagttagagtttacggcaacctttaagcaccaataccttttggcatagtctaaagacctggttcttaattttaaacaaatttaactaaagatttccctatcaaagaagtaacgagttgacagattttctcaaaataaatcgatactgcatttctaggcatatccagcgatctgtcataaaacaatggaattgagacacttgagatacttcgttgccgttgttgaagaacaatcttttacaaaggctgccgacaagttgtgtattgctcaaccaccattatccagacaaatccaaaacttggaagaagaattgggtatccaattattggaaagaggttccagaccagttaagactactccagaaggtcatttcttttaccaatacgccatcaagttgctaagcaacgttgatcaaatggtcagtatgaccaagagaattgcctctgttgaaaagaccattagaatcggttttgttggttccttgttgttcggtttgttgccaagaattatccacttgtacagacaagctcatccaaacttgagaatcgaattatacgaaatgggtactaaggctcaaaccgaagctttgaaagaaggtagaattgacgctggttttggtagattgaagatttctgatccagccatcaagagaaccttgttgagaaacgaaagattgatggttgctgttcatgcttcccatccattgaatcaaatgaaggataagggtgttcacttgaacgatttgatcgacgaaaagatcttgttgtacccatcttctccaaagccaaacttctctactcatgttatgaacatcttctctgaccatggtttggaacctaccaagattaacgaagttagagaagtccaattggccttgggtttggttgctgctggtgaaggtatttcattggttccagcttctacccaatccattcaattattcaacttgtcctacgtcccattattagatccagatgctattaccccaatctacattgctgttagaaacatggaagaatccacctacatctactcattatacgaaaccatcagacaaatctacgcctacgaaggttttactgaaccaccaaattggtaAAGCGGCCGCATTCatcgcgtgcattcatccgctctaaccgaaaaggaaggagttagacaacctgaagtctaggtccctatttatttttttatagttatgttagtattaagaacgttatttatatttcaaatttttcttttttttctgtacagacgcgtgtacgcatgtaacattatactgaaaaccttgcttgagaaggttttgggacgctcgaagatcgcgtacccaattcgccctatagtgagtcg'\n",
    "Sequences['insert_pCCM003']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtATCTAGATCAGAGGGTGGTaaatgaagtgtaatagtattcatttttcttataaatcatcccttccgtgatttatacaaaagaagaggagaatatgctgaatacttggtatattactctacattatactcttatcttgacgggtattctgagcatcttactcagtttcaagatcttttaatgtccaaaaacatttgagccgatctaaatacttctgtgttttcattaatttataaattgtactcttttaagacatggaaagtaccaacatcggttgaaacagtttttcatttacttatggtttattggtttttccagtgaatgattatttgtcgttaccctttcgtaaaagttcaaacacgtttttaagtattgtttagttgctctttcgacatatatgattatccctgcgcggctaaagttaaggatgcaaaaaacataagacaactgaagttaatttacgtcaattaagttttccagggtaatgatgttttgggcttccactaattcaataagtatgtcatgaaatacgttgtgaagagcatccagaaataatgaaaagaaacaacgaaactgggtcggcctgttgtttcttttctttaccacgtgatctgcggcatttacaggaagtcgcgcgttttgcgcagttgttgcaacgcagctacggctaacaaagcctagtggaactcgactgatgtgttagggcctaaaactggtggtgacagctgaagtgaactattcaatccaatcatgtcatggctgtcacaaagaccttgcggaccgcacgtacgaacacatacgtatgctaatatgtgttttgatagtacccagtgatcgcagacctgcaatttttttgtaggtttggaagaatatataaaggttgcactcattcaagatagtttttttcttgtgtgtctattcattttattattgtttgtttaaatgttaaaaaaaccaagaacttagtttcaaaTTAAATTCATCACACAAACAAACAAAACAAAAGCCCTCTtACAATGACTCAATTCACTGACATTGATaagctagccgtctccaccataagaattttggctgtggacaccgtatccaaggccaactcaggtcacccaggtgctccattgggtatggcaccagctgcacacgttctatggagtcaaatgcgcatgaacccaaccaacccagactggatcaacagagatagatttgtcttgtctaacggtcacgcggtcgctttgttgtattctatgctacatttgactggttacgatctgtctattgaagacttgaaacagttcagacagttgggttccagaacaccaggtcatcctgaatttgagttgccaggtgttgaagttactaccggtccattaggtcaaggtatctccaacgctgttggtatggccatggctcaagctaacctggctgccacttacaacaagccgggctttaccttgtctgacaactacacctatgttttcttgggtgacggttgtttgcaagaaggtatttcttcagaagcttcctccttggctggtcatttgaaattgggtaacttgattgccatctacgatgacaacaagatcactatcgatggtgctaccagtatctcattcgatgaagatgttgctaagagatacgaagcctacggttgggaagttttgtacgtagaaaatggtaacgaagatctagccggtattgccaaggctattgctcaagctaagttatccaaggacaaaccaactttgatcaaaatgaccacaaccattggttacggttccttgcatgccggctctcactctgtgcacggtgccccattgaaagcagatgatgttaaacaactaaagagcaaattcggtttcaacccagacaagtcctttgttgttccacaagaagtttacgaccactaccaaaagacaattttaaagccaggtgtcgaagccaacaacaagtggaacaagttgttcagcgaataccaaaagaaattcccagaattaggtgctgaattggctagaagattgagcggccaactacccgcaaattgggaatctaagttgccaacttacaccgccaaggactctgccgtggccactagaaaattatcagaaactgttcttgaggatgtttacaatcaattgccagagttgattggtggttctgccgatttaacaccttctaacttgaccagatggaaggaagcccttgacttccaacctccttcttccggttcaggtaactactctggtagatacattaggtacggtattagagaacacgctatgggtgccataatgaacggtatttcagctttcggtgccaactacaaaccatacggtggtactttcttgaacttcgtttcttatgctgctggtgccgttagattgtccgctttgtctggccacccagttatttgggttgctacacatgactctatcggtgtcggtgaagatggtccaacacatcaacctattgaaactttagcacacttcagatccctaccaaacattcaagtttggagaccagctgatggtaacgaagtttctgccgcctacaagaactctttagaatccaagcatactccaagtatcattgctttgtccagacaaaacttgccacaattggaaggtagctctattgaaagcgcttctaagggtggttacgtactacaagatgttgctaacccagatattattttagtggctactggttccgaagtgtctttgagtgttgaagctgctaagactttggccgcaaagaacatcaaggctcgtgttgtttctctaccagatttcttcacttttgacaaacaacccctagaatacagactatcagtcttaccagacaacgttccaatcatgtctgttgaagttttggctaccacatgttggggcaaatacgctcatcaatccttcggtattgacagatttggtgcctccggtaaggcaccagaagtcttcaagttcttcggtttcaccccagaaggtgttgctgaaagagctcaaaagaccattgcattctataagggtgacaagctaatttcTCCTTTGAAAAAAGCTTTCTGAACACAGGCtGTGAATTTACTTTAAATCTTGCATTTAAATAAATTTTCTTTTTATAGCTTTATGACTTAGTTTCAATTTATATACTATTTTAATGACATTTTCGATTCATTGATTGAAAGCTTTGTGTTTTTTCTTGATGCGCTATTGCATTGTTCTTGTCTTTTTCGCCACATGTAATATCTGTAGTAGATACCTGATACATTGTGGATGCTGAGTGAAATTTTAGTTAATAATGGAGGCGCTCTTAATAATTTTGGGGATATTGGCTTTTTTTTTTAAAGTTTACAAATGAATTTTTTCCGCCAGGATAACGATTCTGAAGTTACTCTTAGCGTTCCTATCGGTACAGCCATCAAATCATGCCTATAAATCATGCCTATATTTGCGTGCAGTCAGTATCATCTACATGAAAAAAACTCCCGCAATTTCTTATAGAATACGTTGAAAATTAAATGTACGCGCCAAGATAAGATAACATATATCTAGATGCAGTAATATACACAGATTCCCGCGGACGTGGGAAGGAAAAAATTAGATAACAAAATCTGAGTGATATGGAAATTCCGCTGTATAGCTCATATCTTTCCCTACCTGCAGAaTCGCGTGcattc'\n",
    "Sequences['insert_pCCM004']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtACTGGTAGAGAGCGACTTTgtatgccccaattgcgaaacccgcgatatccttctcgattctttagtacccgaccaggacaaggaaaaggaggtcgaaacgtttttgaagaaacaagaggaactacacggaagctctaaagatggcaaccagccagaaactaagaaaatgaagttgatggatccaactggcaccgctggcttgaacaacaataccagccttccaacttctgtaaataacggcggtacgccagtgccaccagtaccgttacctttcggtatacctcctttccccatgtttccaatgcccttcatgcctccaacggctactatcacaaatcctcatcaagctgacgcaagccctaagaaatgaataacaatactgacagtactaaataattgcctacttggcttcacatacgttgcatacgtcgatatagataataatgataatgacagcaggattatcgtaatacgtaatagttgaaaatctcaaaaatgtgtgggtcattacgtaaataatgataggaatgggattcttctatttttcctttttccattctagcagccgtcgggaaaacgtggcatcctctctttcgggctcaattggagtcacgctgccgtgagcatcctctctttccatatctaacaactgagcacgtaaccaatggaaaagcatgagcttagcgttgctccaaaaaagtattggatggttaataccatttgtctgttctcttctgactttgactcctcaaaaaaaaaaaatctacaatcaacagatcgcttcaattacgccctcacaaaaacttttttccttcttcttcgcccacgttaaattttatccctcatgttgtctaacggatttctgcacttgatttattataaaaagacaaagacataatacttctctatcaatttcagttattgttcttccttgcgttattcttctgttcttctttttcttttgtcatatataacCATAACCAAGTAATACATATTCAAAAGCCCTCTtACAATGCCATCCAAGTTGGccattacctctatgtctttgggtagatgttatgccggtcattctttcactactaagttggatatggctagaaagtacggttaccaaggtttggaattattccatgaagatttggctgatgtcgcctatagattgtctggtgaaactccatctccatgtggtccatcaccagctgctcaattgtctgctgctagacaaattttgagaatgtgccaagtcagaaacatcgaaatcgtttgcttgcaaccattctctcaatacgatggtttgttggatagagaagaacacgaaagaagattggaacaattggaattctggatcgaattggcccatgaattggataccgatattattcaaattccagccaacttcttgccagccgaagaagttactgaagatatctctttgattgtctccgacttgcaagaagtagctgatatgggtttacaagctaacccaccaattagattcgtttacgaagctttgtgttggtccactagagttgatacttgggaaagatcttgggaagttgttcaaagagttaacagaccaaacttcggtgtttgtttggacacttttaacattgccggtagagtttatgctgatccaactgttgcttctggtagaactccaaatgctgaagaagctatcagaaagtccattgccagattggttgaaagagttgacgtttccaaggttttctacgttcaagttgttgatgccgaaaagttgaagaaaccattggttccaggtcacagattctatgatccagaacaaccagctagaatgtcttggtctagaaactgcagattattctacggtgaaaaggatagaggtgcttacttgccagtaaaagaaattgcttgggcttttttcaacggtttgggttttgaaggttgggtttccttagaattattcaacagaagaatgtccgataccggttttggtgttccagaagaattagctagaagaggtgctgtttcttgggctaaattggttagagatatgaagatcaccgttgactctccaactcaacaacaagctacacaacaacctatcagaatgttgtCTTTGTCAGCTGCTTTGTGAACACAGGCtATAGATTAATTTAAACAGTATATGTACAGTTTtatatatatatatatatatatatacatatataaagaaacctgtgcgttttttgtattttcaaatacatttagttttggcgccacttcTATAAAAGGTCTCATGATATTGTTACatcgcgtgcattc'\n",
    "Sequences['insert_pCCM005']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtAAGGATGAGCCAAGAATAAGGgaacaagattttggtaatttccaaaaaatcaatagcatgcaggacgttatgaagaagagatctacgtatggtcatttcttcttcagattccctcatggagaaagtgcggcagatgtatatgacagagtcgccagtttccaagagactttattcaggcacttccatgataggcaagagagaagacccagagatgttgttgtcctagttacacatggtatttattccagagtattcctgatgaaatggtttagatggacatacgaagagtttgaatcgtttaccaatgttcctaacgggagcgtaatggtgatggaactggacgaatccatcaatagatacgtcctgaggaccgtgctacccaaatggactgattgtgagggagacctaactacatagtgtttaaagattacggatatttaacttacttagaataatgccatttttttgagttataataatcctacgttagtgtgagcgggatttaaactgtgaggaccttaatacattcagacacttctgcggtatcaccctacttattcccttcgagattatatctaggaacccatcaggttggtggaagattacccgttctaagacttttcagcttcctctattgatgttacacctggacaccccttttctggcatccagtttttaatcttcagtggcatgtgagattctccgaaattaattaaagcaatcacacaattctctcggataccacctcggttgaaactgacaggtggtttgttacgcatgctaatgcaaaggagcctatatacctttggctcggctgctgtaacagggaatataaagggcagcataatttaggagtttagtgaacttgcaacatttactattttcccttcttacgtaaatatttttctttttaattctaaatcaatctttttcaattttttgtttgtattcttttcttgcttaaatctataACTACAAAAAACACATACATAAACTAAAAAGCCCTCTtACCATGGGTACCACTCTtgacgacacggcttaccggtaccgcaccagtgtcccgggggacgccgaggccatcgaggcactggatgggtccttcaccaccgacaccgttttccgcgtcaccgccaccggggacggcttcaccctgcgggaggtgccggtggacccgcccctgaccaaggtgttccccgacgacgaatcggacgacgaatcggacgacggggaggacggcgacccggactcccggacgttcgtcgcgtacggggacgacggcgacctggcgggcttcgtggtcgtctcgtactccggctggaaccgccggctgaccgtcgaggacatcgaggtcgccccggagcaccgggggcacggggtcgggcgcgcgttgatggggctcgcgacggagttcgcccgcgagcggggcgccgggcacctctggctggaggtcaccaacgtcaacgcaccggcgatccacgcgtaccggcggatggggttcaccctctgcggcctggacaccgccctgtacgacggcaccgcctcggacggcgagcaggcgctctacatgagcaTGCCCTGCCCCTAAACACAGGCtGCTTCTCGAGAAAAACAAAAGAGTTAataataaagtatatatgcttttttactattaataaagtttcttattttccctacatgtatacatacatataaatatactcttttGGAAAAAATTTCTTTTTTTTTTTTTTAATTTTatcgcgtgcattc'\n",
    "Sequences['insert_pCCM006']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtCAGCATTTTCAAAGGTGTgttcttcgtcagacatgttttagtgtgtgaatgaaataggtgtatgttttctttttgctagacaataattaggaacaaggtaagggaactaaagtgtagaataagattaaaaaagaagaacaagttgaaaaggcaagttgaaatttcaagaaaaaagtcaattgaagtacagtaaattgacctgaatatatctgagttccgacaacaatgagtttaccaaagagaacaatggaataggaaactttgaacgaagaaaggaaagcaggaaaggaaaaaatttttaggctcgagaacaatagggcgaaaaaacaggcaacgaacgaacaatggaaaaacgaaaaaaaaaaaaaaaaacacagaaaagaatgcagaaagatgtcaactgaaaaaaaaaaaggtgaacacaggaaaaaaaataaaaaaaaaaaaaaaaaaaggaggacgaaacaaaaaagtgaaaaaaaatgaaaatttttttggaaaaccaagaaatgaattatatttccgtgtgagacgacatcgtcgaatatgattcagggtaacagtattgatgtaatcaatttcctacctgaatctaaaattcccgggagcaagatcaagatgttttcaccgatctttccggtctctttggccggggtttacggacgatggcagaagaccaaagcgccagttcatttggcgagcgttggttggtggatcaagcccacgcgtaggcaatcctcgagcagatccgccaggcgtgtatatatagcgtggatggccaggcaactttagtgctgacacatacaggcatatatatatgtgtgcgacgacacatgatcatatggcatgcatgtgctctgtatgtatataaaactcttgttttcttcttttctctaaatattctttccttatacattaggacctttgcagcataaattactatacttctatagacacacaAACACAAATACACACACTAAATTAATAAGCCCTCTtACAATGTCCCAAGCTTTCAccgaatctgttaagacttctttgggtccaaatgctactccaagagctaaaaagttgattgcctctttggttcaacacgttcatgatttcgctagagaaaaccatttgactaccgaagattggttgtggggtgttgatttcattaacagaattggtcaaatgtccgactccagaagaaacgaaggtattttggtttgcgatatcatcggtttggaaaccttggttgatgctttgactaacgaatccgaacaatctaaccatacctcctctgctattttgggtcctttttacttgccagattctccagtttatccaaacggtggttctatcgttcaaaaggctattccaactgatgttaagtgcttcgttagaggtaaggttactgatactgaaggtaaaccattgggtggtgctcaattggaagtttggcaatgtaattctgctggtttctactctcaacaagctgatcatgatggtccagaattcaatttgagaggtactttcattaccgacgacgaaggtaattactccttcgaatgtttaagaccaacctcctatccaattccatacgatggtcctgctggtgatttgttgaaaatcatggatagacatccaaacagaccatcccatattcattggagagtttctcatccaggttaccatactttgatcacccaaatctatgatgctgaatgtccatacaccaacaacgattctgtttacgctgttaaggatgacatcatcgttcacttcgaaaaggttgataacaaggataaggatttggtcggtaaggtcgaatacaagttggattacgatatttccttggccaccgaatcctctattcaagaagctagagctgctgctaaagctagaCAAGATGCTGAAATCAAGTTGTAAACACAGGCtGCGCAATGATTGAATAGTCAAAgattttttttttttaattttttttttttaattttttttttttttcatagaactttttatttaaataaatcacgtctatatatgtatcagtataacgtaaaaaaaaaaacaccgtcagttaaacaaaacataaataaaaaaaaAAAGAAGTGTCAAATCAAGTGTCAAATCatcgcgtgcattc'\n",
    "Sequences['insert_pCCM007']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtGCTATAAAAAACACGCTTTTTCAgttcgagtttatcattatcaatactgccatttcaaagaatacgtaaataattaatagtagtgattttcctaactttatttagtcaaaaaattagccttttaattctgctgtaacccgtacatgcccaaaatagggggcgggttacacagaatatataacatcgtaggtgtctgggtgaacagtttattcctggcatccactaaatataatggagcccgctttttaagctggcatccagaaaaaaaaagaatcccagcaccaaaatattgttttcttcaccaaccatcagttcataggtccattctcttagcgcaactacagagaacaggggcacaaacaggcaaaaaacgggcacaacctcaatggagtgatgcaacctgcctggagtaaatgatgacacaaggcaattgacccacgcatgtatctatctcattttcttacaccttctattaccttctgctctctctgatttggaaaaagctgaaaaaaaaggttgaaaccagttccctgaaattattcccctacttgactaataagtatataaagacggtaggtattgattgtaattctgtaaatctatttcttaaacttcttaaattctacttttatagttagtcttttttttagttttaaaacaccaagaacttagtttcgaataaacacacataaacaaacaaaagtgcaggtagtgcaggtaaaacaatgaagttgatcatcggtatgactggtgctacaggtgctccattgggtgttgctttgttgcaagctttgagagatatgccagaagttgaaacccatttggttatgtctaaatgggctaagaccaccattgaattggaaactccatggactgctagagaagttgctgctttggctgatttttctcattctccagctgatcaagctgctactatttcttctggttctttcagaactgatggtatgatcgttattccatgctctatgaaaaccttggctggtattagagctggttatgctgaaggtttggttggtagagctgctgatgttgttttgaaagaaggtagaaagttggtcttggtcccaagagaaatgccattgtctactatccatttggaaaacatgttggccttgtctagaatgggtgtagctatggttccaccaatgccagcttattacaatcatccagaaaccgttgatgacatcaccaaccatatagttaccagagttttggaccaattcggtttggattatcacaaagctagaagatggaacggtttgagaactgctgaacaattcgctcaagaaattgaatgaatCGCACGCATTCCGTTGACACAGGCtTCACATATGAAAGTATATACCCGcttttgtacactatgtagctataattcaatcgtattattgtagctccgcacgaccatgccttagaaataTCCGCAGCGCGCatcgcgtgcattc'\n",
    "Sequences['insert_pCCM008']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtGCACACACCATAGCTTCAAaatgtttctactccttttttactcttccagattttctcggactccgcgcatcgccgtaccacttcaaaacacccaagcacagcatactaaatttcccctctttcttcctctagggtgtcgttaattacccgtactaaaggtttggaaaagaaaaaagagaccgcctcgtttctttttcttcgtcgaaaaaggcaataaaaatttttatcacgtttctttttcttgaaaatttttttttttgatttttttctctttcgatgacctcccattgatatttaagttaataaacggtcttcaatttctcaagtttcagtttcatttttcttgttctattacaactttttttacttcttgctcattagaaagaaagcatagcaatctaatctaagttttaattacaaatctgtcatatctgtcataaaacaatgaccgccccaatccaagatttgagagatgctattgctttgttacaacaacacgacaatcaatacttggaaaccgatcatccagttgatccaaatgctgaattggctggtgtttacagacatattggtgctggtggtactgtaaaaagaccaactagaattggtccagccatgatgttcaacaacattaagggttatccacactccagaatcttggttggtatgcatgcttctagacaaagagcagctttgttgttgggttgtgaagcttctcaattggctttggaagttggtaaagctgttaagaaaccagttgctccagttgttgttccagcttcttctgctccatgtcaagaacaaattttcttggctgatgatccagacttcgatttgagaactttgttgccagctcataccaacactccaattgatgctggtccatttttttgtttgggtttggctttagcttctgatcctgttgatgcttctttgaccgatgttaccattcatagattgtgcgttcaaggtagagatgaattgtctatgtttttggctgccggtagacatatcgaagtttttagacaaaaagctgaagctgctggtaagccattgccaattactattaacatgggtttagatccagccatctacattggtgcttgttttgaagctccaactactccatttggttacaacgaattgggtgttgctggtgctttgagacaaagaccagttgaattggttcaaggtgtttctgttccagaaaaggctattgctagagccgaaatagttatcgaaggtgaattattgccaggtgtcagagttagagaagatcaacatacaaattccggtcatgctatgccagaatttccaggttattgtggtggtgctaatccatctttgccagttattaaggttaaggccgttaccatgagaaacaacgctattttacaaactttggtcggtccaggtgaagaacatacaactttggctggtttgccaaccgaagcttctatttggaatgctgttgaagctgcaattccaggtttcttgcaaaatgtttatgctcatacagctggtggtggtaagttcttgggtatattgcaagtcaagaaaagacaaccagctgacgaaggtagacaaggtcaagctgctttattagctttggctacttactccgaattgaagaatatcatcttggtcgatgaagatgttgatatcttcgattccgatgatattttgtgggctatgactactagaatgcaaggtgatgtttccattactaccattccaggtattagaggtcaccaattagatccatctcaaaccccagaatactccccatcaattagaggtaatggtatctcctgtaagaccattttcgattgcactgttccatgggctttgaagtctcattttgaaagagcaccatttgctgacgttgatcctagaccttttgctccagaatatttcgctagattggaaaagAATCAAGGTTCCGCTAAGTAAACACAGGCtTCGAATTTACGTAGCCCAATCTAccacttttttttttcattttttaaagtgttatacttagttatgctctaggataatgaactacttttttttttttttttttactgttatcataaatatatataccttattgttgtttgcaaccgtcggttaattccttatcaaggttccCCAAGTTCGGATCATTACCATCatcgcgtgcattc'\n",
    "Sequences['insert_pCCM009']='caatctggcggcttgagttctcaacatgttttattttttacttatattgctggtagggtaaaaaaatataactcctaggaataggttgtctatatgtttttgtcttgcttctataattgtaacaaacaaggaaagggaaaatactgggtgtaaaagccattgagtcaagttaggtcatcccttttatacaaaatttttcaattttttttccaagattcttgtacgattaattattttttttttgcgtcctacagcgtgatgaaaatttcgcctgctgcaagatgagcgggaacgggcgaaatgtgcacgcgcacaacttacgaaacgcggatgagtcactgacagccaccgcagaggttctgactcctactgagctctattggaggtggcagaaccggtaccggaggaggccgctataaccggtttgaatttattgtcacagtgtcacatcagcattaagtcctcagcgagctcgcatggaatgcgtgcgatgagcgacctcatgctatacctgagaaagcaacctgacctacaggaaagagttactcaagaataagaattttcgttttaaaacctaagagtcactttaaaatttgtatacacttattttttttataacttatttaataataaaaatcataaatcataagaaattcgcttatttagaagtgtcaacaacgtatctaccaacggaatgCGTGCGAtAAAGAAACTTAATACGTTATGCCgtaatgaagggctaccaaaaacgataatctcaactgtaaacaggtacaatgcggacccttttgccacaaaacatacatcattcattgccggaaaaagaaagaagtgaagacagcagtgcagccagccatgttgcgccaatctaattatagatgctggtgccctgaggatgtatctggagccagccatggcatcatgcgctaccgccggatgtaaaatccgacacgcaaaagaaaaccttcgaggttgcgcacttcgcccacccatgaaccacacggttagtccaaaaggggcagttcagattccagatgcgggaattagcttgctgccaccctcacctcactaacgctgcggtgtgcggatacttcatgctatttatagacgcgcgtgtcggaatcagcacgcgcaagaaccaaatgggaaaatcggaatgggtccagaactgctttgagtgctggctattggcgtctgatttccgttttgggaatcctttgccgcgcgcccctctcaaaactccgcacaagtcccagaaagcgggaaagaaataaaacgccaccaaaaaaaaaaaaataaaagccaatcctcgaagcgtgggtggtaggccctggattatcccgtacaagtatttctcaggagtaaaaaaaccgtttgttttggaattccccatttcgcggccacctacgccgctatctttgcaacaactatctgcgataactcagcaaattttgcatattcgtgttgcagtattgcgataatgggagtcttacttccaacataacggcagaaagaaatgtgagaaaattttgcatcctttgcctccgttcaagtatataaagtcggcatgcttgataatctttctttccatcctacattgttctaattattcttattctcctttattctttcctaacataccaagaaattaatcttctgTCATTCGCTTAAACACTATATCAATAAGCCCTCTtACAATGATCTGTCCAAGATGCgccgacgaaaaaattgaagttatggctacttctccagttaagggtgtttggactgtttatcaatgtcaacactgcttgtacacttggagagatactgaaccattgagaagaacctctagagaacattaccctgaagctttcagaatgacccaaaaggatattgatgaagctccacaagttcctcatgttccacCATTATTGCCAGAAGATAAGAGATAAACACAGGCtACAGAAGACGGGAGACACtagcacacaactttaccaggcaaggtatttgacgctagcatgtgtccaattcagtgtcatttatgattttttgtagtaggatataaatatatacagcgctccaaatagtgcggttgccccaaaaacaccacggaacctcatctgttctcgtactttgttgtgacaaagtagctcactgccttattatcacattttcattatgcaacgctTCGGAAAATACGATGTTGAAAATatcgcgtgcattc'\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "insert_pCCM001\n",
      "Has len 1953\n",
      "... Done\n",
      "insert_pCCM002\n",
      "Has len 2976\n",
      "... Done\n",
      "insert_pCCM003\n",
      "Has len 4373\n",
      "... Done\n",
      "... Done\n",
      "insert_pCCM004\n",
      "Has len 2988\n",
      "... Done\n",
      "insert_pCCM005\n",
      "Has len 2454\n",
      "... Done\n",
      "insert_pCCM006\n",
      "Has len 2830\n",
      "... Done\n",
      "insert_pCCM007\n",
      "Has len 2168\n",
      "... Done\n",
      "insert_pCCM008\n",
      "Has len 2873\n",
      "... Done\n",
      "insert_pCCM009\n",
      "Has len 2206\n",
      "... Done\n"
     ]
    }
   ],
   "source": [
    "Seq=np.empty((0,2), dtype=object)\n",
    "i=1\n",
    "for name, seq in Sequences.items():\n",
    "    print('insert_pCCM00'+str(i))\n",
    "    Primers = design_sequencing_primers(Sequences['insert_pCCM00'+str(i)])\n",
    "    for p,S in Primers.items():\n",
    "        Seq=np.vstack([Seq,['pCCM00'+str(i),S]])\n",
    "    i+=1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "21 Primers were designed\n"
     ]
    }
   ],
   "source": [
    "#delete repeating primers but keep associated plasmid name\n",
    "i2del=[]\n",
    "name=''\n",
    "for i,S in enumerate(Seq[:,1]):\n",
    "    \n",
    "    if (S==Seq[:,1]).sum()>1:\n",
    "        i2del.append(i)\n",
    "        name+=Seq[i,0]+ ' '\n",
    "#change name of first occurance delete all other occurances\n",
    "Seq[i2del[0],0]=name\n",
    "Seq = np.delete(Seq, (i2del[1:]), axis=0)\n",
    "print(str(len(Seq))+ ' Primers were designed')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "#copy to clipboard the primer list\n",
    "#Copy=pd.DataFrame(Seq,  columns=['Template', 'Seq'])\n",
    "Copy=''\n",
    "for i in range(len(Seq)):\n",
    "    Copy+='CCM.S'+str(i+1).zfill(3) + '\\t' + Seq[i,1] + '\\t' +Seq[i,0] +'\\n'\n",
    "pyperclip.copy(Copy)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CAX4\n",
      "Has len 2269\n",
      "... Done\n"
     ]
    }
   ],
   "source": [
    "Sequences={}\n",
    "Sequences['CAX4']='tttatatattgccctcaaaactgtatctcatctttttttctgcaatccttgctttcgtaatctaagtgtgggtgacatgctaaatccgcggctttccttaagctttttcacaaaccatctattatgtccagaagctccgctgattatccgtggaaaagggtcttattctgccgtaggaaacttcttctcgagaaaaaagtgagttcacccgcggcgctctcgtaaaacccgagggccgattctttccctccgtggaacaatcggccccgcggcgtcagagggtattatctccgcaagtgatagaactcacatttattctacgttctgcatggttttgattatcttcttttgcacgatgtcacatactttttcgattaccgtcgctttacacagtaactgtttaaaacgagcgttcttaattaataactgtaggagagcaggctttcggctttctttatgagaaataaggactactccagcttgccaagttttatccagttacacaaacgctcaagatcgcctcgctaaaatagatgaaaaaataagaaaaatgaaatgttcaacctaatcccttttggatttatcattgaaagatcgctgatttattcttttccaatacgcctcgtaattctctttcaatgtcaaaggcgccagattgtaagaatctgtcatgtaaaataatctgacaatacgtagttttaaaaaccaattgattaaaccaagctctcttatgatgccaactataaaaaaataaagtgatccagtcagtgcccccacgctgaatcccacgattacttgatctaaattgtggtagtgcaagtaaactctggaaaagcaaacgcaaaacgataataaagccaatgcaccagaaaaaatgcatttttctaagaagtttagattcttccaggaagtgtatatcttcagagagttataggtaaaacaaaaccccatgaattgggagtgtgcactgggcatcccgtaaccggatcttatagtgtcattttggaacgacgcaccgaacgatacggggcgtggctgttttattatattcttgatcacgttattgaatatttcgttcatcaattggccaaaggctacaatgcaggcttctaactctcttgtgatgataaaccacgacaaataaaaagctagcactaggatgggcatcagcgagaaatatgcactaaggaatgatagaaagtcatgcgaatcatagagaatgtatgtgtcatcgaatggtataacatttggatttggatttattgcagcggcggtactattcatgatatgatccgattcaaaacaaattttgatgtagataaaatgcctggtataatgagtggtagagaagaaaattagacgaaaagaatgagaacgaagaaatgatttaaagtgatcacagtggcaatcactttcccctttttaacgcgtgttgagcaatcgattgatgtctctaccatatgtagcattttctcagaaggcaaacttttctttttctttctacttttccaacaagaaattttaagttttcccagaaacccgaattctcctatttcatccaccacgtaagaacggttttcttcctggcgtaattaaaagcataaagaaaaactgaacaagctctagatgtagatcagggtatacatggtgcgcttcagtaagtgtactgtaccactagtttggcgtctgtcacttgaattgcggatttgtgtagagcaatgaaagcgctgcttctgccgccatcaaaaaaaactgagtagttattaaagcctatgtatgacaatataaaaatgtatacagatcagtctgtatataaatcatgaaaatatctttaaaaatttcaagagcgtgtttccgctaaaccttgtcatattcaacacaaatcagtatcattctcggcgtaaattacatgcgaatctccctaattgtgattcaatattccagcgaaccccgagaatttaaatagaacagagtatatgcatttattaacagttattacgccttgtccccagggagagtagtaagggatatgggcatttataaatgtacataagtcacgtttttgcagccaataaaatataataatagaatagtaacaaggaaagctaggccaaaactccttacatggagctagtataccccttttctaagaggagtacttggcaatcagttgatcaacaagggcaatgtattccttttcggcatcttcctgggatttaccttttaagttttcccaggcttcccacttgtagcggtccttcatgttgaa'\n",
    "\n",
    "\n",
    "Seq=np.empty((0,2), dtype=object)\n",
    "i=1\n",
    "for name, seq in Sequences.items():\n",
    "    print(name)\n",
    "    Primers = design_sequencing_primers(Sequences[name])\n",
    "    for p,S in Primers.items():\n",
    "        Seq=np.vstack([Seq,[name,S]])\n",
    "    i+=1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "#copy to clipboard the primer list\n",
    "#Copy=pd.DataFrame(Seq,  columns=['Template', 'Seq'])\n",
    "Copy=''\n",
    "for i in range(len(Seq)):\n",
    "    Copy+='CCM.S'+str(i+1).zfill(3) + '\\t' + Seq[i,1] + '\\t' +Seq[i,0] +'\\n'\n",
    "pyperclip.copy(Copy)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<ipython-input-22-253357ea63c6>, line 1)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-22-253357ea63c6>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    CCM.S001\tTCTAAGTGTGGGTGACATGC\tCAX4\u001b[0m\n\u001b[0m            \t                   ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "CCM.S001\tTCTAAGTGTGGGTGACATGC\tCAX4\n",
    "CCM.S002\tCGCAATTCAAGTGACAGACG\tCAX4\n",
    "CCM.S003\tCAATCGATTGATGTCTCTACC\tCAX4\n"
   ]
  }
 ],
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