YeastPathwayKit_project_from_name.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pydna.amplify import Anneal\n",
    "from pydna.amplify import pcr\n",
    "from pydna.assembly import Assembly\n",
    "from pydna.genbank import genbank\n",
    "from pydna.genbank import Genbank\n",
    "from pydna.download import download_text\n",
    "from pydna.dseqrecord import Dseqrecord\n",
    "from pydna.dseq import Dseq\n",
    "from pydna.readers import read\n",
    "from pydna.readers import read_primer\n",
    "from pydna.parsers import parse\n",
    "from pydna.parsers import parse_primers\n",
    "from pydna.editor import ape\n",
    "from pydna.design import primer_design\n",
    "from pydna.design import assembly_fragments\n",
    "from pydna.design import circular_assembly_fragments\n",
    "from pydna.utils import eq\n",
    "from pydna.genbankfixer import gbtext_clean\n",
    "from pydna.myprimers import PrimerList"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "from joblib import Memory\n",
    "memory = Memory(location=f\"{sys.path[0]}/joblib_memory_cachedir\", verbose=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pydna.amplify import pcr\n",
    "from pydna.parsers import parse\n",
    "from pydna.design import primer_design\n",
    "\n",
    "from pydna.genbankrecord import GenbankRecord\n",
    "from IPython.display import display_markdown"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "sequence_library_path = Path(\"sequences\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [],
   "source": [
    "orfs = parse(\"\"\"\\\n",
    "\n",
    ">ATF1 uSEGUID r8BaXu2MdYByHuhSYXBNKXIxIfg\n",
    "ATGAATGAAATCGATGAGAAAAATCAGGCCCCCGTGCAACAAGAATGCCTGAAAGAGATGATTCAGAATGGGCATGCTCGGCGTATGGGATCTGTTGAAGATCTGTATGTTGCTCTCAACAGACAAAACTTATATCGAAACTTCTGCACATATGGAGAATTGAGTGATTACTGTACTAGGGATCAGCTCACATTAGCTTTGAGGGAAATCTGCCTGAAAAATCCAACTCTTTTACATATTGTTCTACCAACAAGATGGCCAAATCATGAAAATTATTATCGCAGTTCCGAATACTATTCACGGCCACATCCAGTGCATGATTATATTTCAGTATTACAAGAATTGAAACTGAGTGGTGTGGTTCTCAATGAACAACCTGAGTACAGTGCAGTAATGAAGCAAATATTAGAAGAATTCAAAAATAGTAAGGGTTCCTATACTGCAAAAATTTTTAAACTTACTACCACTTTGACTATTCCTTACTTTGGACCAACAGGACCGAGTTGGCGGCTAATTTGTCTTCCAGAAGAGCACACAGAAAAGTGGAAAAAATTTATCTTTGTATCTAATCATTGCATGTCTGATGGTCGGTCTTCGATCCACTTTTTTCATGATTTAAGAGACGAATTAAATAATATTAAAACTCCACCAAAAAAATTAGATTACATTTTCAAGTACGAGGAGGATTACCAATTATTGAGGAAACTTCCAGAACCGATCGAAAAGGTGATAGACTTTAGACCACCGTACTTGTTTATTCCGAAGTCACTTCTTTCGGGTTTCATCTACAATCATTTGAGATTTTCTTCAAAAGGTGTCTGTATGAGAATGGATGATGTGGAAAAAACCGATGATGTTGTCACCGAGATCATCAATATTTCACCAACAGAATTTCAAGCGATTAAAGCAAATATTAAATCAAATATCCAAGGTAAGTGTACTATCACTCCGTTTTTACATGTTTGTTGGTTTGTATCTCTTCATAAATGGGGTAAATTTTTCAAACCATTGAACTTCGAATGGCTTACGGATATTTTTATCCCCGCAGATTGCCGCTCACAACTACCAGATGATGATGAAATGAGACAGATGTACAGATATGGCGCTAACGTTGGATTTATTGACTTCACCCCCTGGATAAGCGAATTTGACATGAATGATAACAAAGAAAATTTTTGGCCACTTATTGAGCACTACCATGAAGTAATTTCGGAAGCTTTAAGAAATAAAAAGCATCTCCATGGCTTAGGGTTCAATATACAAGGCTTCGTTCAAAAATATGTGAACATTGACAAGGTAATGTGCGATCGTGCCATCGGGAAAAGACGCGGAGGTACATTGTTAAGCAATGTAGGTCTGTTTAATCAGTTAGAGGAGCCCGATGCCAAATATTCTATATGCGATTTGGCATTTGGCCAATTTCAAGGATCCTGGCACCAAGCATTTTCCTTGGGTGTTTGTTCGACTAATGTAAAGGGGATGAATATTGTTGTTGCTTCAACAAAGAATGTTGTTGGTAGTCAAGAATCTCTCGAAGAGCTTTGCTCCATTTACAAAGCTCTCCTTTTAGGCCCTTAG\n",
    "\n",
    ">CTT1 uSEGUID unRT3TWPEXorUhgOrGZRvwcsZwU\n",
    "ATGAACGTGTTCGGTAAAAAAGAAGAAAAGCAAGAAAAAGTTTACTCTCTACAAAACGGTTTTCCGTACTCTCATCACCCATACGCTTCTCAATACTCAAGACCAGACGGCCCTATCTTACTGCAAGACTTCCATCTGCTGGAAAATATCGCAAGTTTCGATAGAGAAAGAGTTCCGGAGCGTGTAGTCCATGCCAAAGGTGGTGGTTGTAGACTGGAGTTCGAACTAACAGATTCTTTGAGTGATATTACATACGCCGCTCCATACCAGAATGTGGGTTACAAATGTCCTGGTCTTGTTCGTTTTTCCACCGTTGGTGGTGAAAGTGGTACACCAGACACTGCAAGAGACCCAAGAGGTGTTTCTTTTAAATTCTATACCGAGTGGGGGAACCATGACTGGGTCTTCAACAATACTCCCGTCTTCTTCCTCAGAGACGCTATTAAGTTTCCCGTATTTATTCATTCGCAAAAGAGAGACCCTCAGTCTCATCTGAATCAGTTTCAGGACACTACCATATACTGGGATTATCTAACATTGAATCCGGAATCAATCCATCAAATAACTTACATGTTTGGTGATAGAGGTACTCCTGCTTCGTGGGCTAGTATGAACGCGTACTCTGGTCATTCCTTCATCATGGTCAACAAAGAAGGTAAGGACACATATGTGCAATTCCACGTCTTGTCGGATACTGGTTTTGAAACCTTGACTGGAGATAAGGCTGCTGAACTGTCAGGCTCCCACCCTGATTATAATCAGGCAAAGCTGTTCACTCAATTGCAAAATGGCGAAAAGCCAAAATTTAACTGTTATGTGCAAACAATGACACCCGAACAAGCAACTAAGTTCAGGTATTCGGTAAATGACCTAACGAAAATATGGCCACACAAGGAATTCCCTTTGAGAAAATTTGGTACCATCACCCTAACGGAGAATGTTGACAATTATTTCCAAGAAATTGAACAAGTTGCATTCAGTCCAACGAACACTTGTATCCCAGGTATTAAGCCTTCTAATGATTCCGTTCTACAAGCCAGACTTTTCTCCTATCCAGACACTCAACGTCATAGATTGGGAGCCAACTATCAGCAATTGCCCGTCAACAGACCAAGAAACTTGGGATGTCCATACTCCAAAGGTGATTCCCAATACACTGCCGAACAGTGTCCATTTAAAGCAGTGAACTTCCAAAGGGACGGCCCAATGAGTTACTACAATTTCGGTCCTGAGCCAAATTATATTTCCAGTTTACCAAATCAAACTCTGAAATTCAAAAATGAAGACAACGACGAAGTATCTGATAAGTTCAAAGGGATAGTTCTTGACGAAGTAACAGAAGTTTCTGTGAGAAAACAGGAACAAGACCAAATCAGAAACGAGCATATTGTTGATGCCAAAATTAATCAATATTACTACGTTTATGGTATTAGTCCACTAGACTTCGAACAGCCAAGAGCTCTATATGAAAAGGTATACAACGATGAACAGAAGAAATTATTCGTTCATAACGTTGTTTGCCACGCTTGTAAGATCAAAGATCCTAAAGTCAAAAAGAGAGTTACGCAATACTTTGGTTTGCTAAACGAAGATTTGGGTAAAGTCATTGCAGAAGGCTTGGGAGTTCCTTGGGAACCTGTTGACCTTGAAGGTTATGCCAAGACTTGGTCCATTGCAAGTGCCAATTAA\n",
    "\n",
    "\"\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "@memory.cache\n",
    "def genbank_accession(s:str):\n",
    "    \n",
    "    from Bio.Blast import NCBIWWW\n",
    "    from Bio.Blast import NCBIXML\n",
    "\n",
    "    result_handle = NCBIWWW.qblast(\"blastn\",\n",
    "                                   \"nt\",\n",
    "                                    s,\n",
    "                                    hitlist_size=10,\n",
    "                                    alignments = 1,\n",
    "                                    expect=1e-8)\n",
    "\n",
    "    blast_records = NCBIXML.read(result_handle)\n",
    "\n",
    "    results = []\n",
    "    length = len(s)\n",
    "\n",
    "    for alignment in blast_records.alignments:\n",
    "        \n",
    "        for hsp in alignment.hsps:\n",
    "            \n",
    "            if hsp.identities == length: # only **perfect** matches !\n",
    "                \n",
    "                results.append((alignment.accession, *sorted((hsp.sbjct_start, hsp.sbjct_end))))\n",
    "\n",
    "    return results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "# ATF1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "    <thead>\n",
       "        <tr>\n",
       "            <th>cds</th>\n",
       "            <th>len</th>\n",
       "            <th>cai</th>\n",
       "            <th>gc</th>\n",
       "            <th>sta</th>\n",
       "            <th>stp</th>\n",
       "            <th>n-end</th>\n",
       "            <th>CGA</th>\n",
       "            <th>CGG</th>\n",
       "            <th>CGC</th>\n",
       "            <th>CCG</th>\n",
       "            <th>CTC</th>\n",
       "            <th>GCG</th>\n",
       "            <th>rare</th>\n",
       "        </tr>\n",
       "    </thead>\n",
       "    <tbody>\n",
       "        <tr>\n",
       "            <td>ATG...TAG</td>\n",
       "            <td>526.0</td>\n",
       "            <td>0.738</td>\n",
       "            <td>0.377</td>\n",
       "            <td>1.0</td>\n",
       "            <td>0.23</td>\n",
       "            <td>3 min</td>\n",
       "            <td>1</td>\n",
       "            <td>4</td>\n",
       "            <td>3</td>\n",
       "            <td>5</td>\n",
       "            <td>6</td>\n",
       "            <td>1</td>\n",
       "            <td>0.038</td>\n",
       "        </tr>\n",
       "    </tbody>\n",
       "</table>"
      ],
      "text/markdown": [
       "|    cds    |  len  |  cai  |   gc  | sta | stp  | n-end | CGA | CGG | CGC | CCG | CTC | GCG |  rare |\n",
       "|:---------:|:-----:|:-----:|:-----:|:---:|:----:|:-----:|:---:|:---:|:---:|:---:|:---:|:---:|:-----:|\n",
       "| ATG...TAG | 526.0 | 0.738 | 0.377 | 1.0 | 0.23 | 3 min |  1  |  4  |  3  |  5  |  6  |  1  | 0.038 |"
      ],
      "text/plain": [
       "+-----------+-------+-------+-------+-----+------+-------+-----+-----+-----+-----+-----+-----+-------+\n",
       "|    cds    |  len  |  cai  |   gc  | sta | stp  | n-end | CGA | CGG | CGC | CCG | CTC | GCG |  rare |\n",
       "+-----------+-------+-------+-------+-----+------+-------+-----+-----+-----+-----+-----+-----+-------+\n",
       "| ATG...TAG | 526.0 | 0.738 | 0.377 | 1.0 | 0.23 | 3 min |  1  |  4  |  3  |  5  |  6  |  1  | 0.038 |\n",
       "+-----------+-------+-------+-------+-----+------+-------+-----+-----+-----+-----+-----+-----+-------+"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/markdown": [
       "# CTT1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "    <thead>\n",
       "        <tr>\n",
       "            <th>cds</th>\n",
       "            <th>len</th>\n",
       "            <th>cai</th>\n",
       "            <th>gc</th>\n",
       "            <th>sta</th>\n",
       "            <th>stp</th>\n",
       "            <th>n-end</th>\n",
       "            <th>CGA</th>\n",
       "            <th>CGG</th>\n",
       "            <th>CGC</th>\n",
       "            <th>CCG</th>\n",
       "            <th>CTC</th>\n",
       "            <th>GCG</th>\n",
       "            <th>rare</th>\n",
       "        </tr>\n",
       "    </thead>\n",
       "    <tbody>\n",
       "        <tr>\n",
       "            <td>ATG...TAA</td>\n",
       "            <td>563.0</td>\n",
       "            <td>0.767</td>\n",
       "            <td>0.413</td>\n",
       "            <td>1.0</td>\n",
       "            <td>0.47</td>\n",
       "            <td>3 min</td>\n",
       "            <td>0</td>\n",
       "            <td>0</td>\n",
       "            <td>0</td>\n",
       "            <td>3</td>\n",
       "            <td>1</td>\n",
       "            <td>1</td>\n",
       "            <td>0.009</td>\n",
       "        </tr>\n",
       "    </tbody>\n",
       "</table>"
      ],
      "text/markdown": [
       "|    cds    |  len  |  cai  |   gc  | sta | stp  | n-end | CGA | CGG | CGC | CCG | CTC | GCG |  rare |\n",
       "|:---------:|:-----:|:-----:|:-----:|:---:|:----:|:-----:|:---:|:---:|:---:|:---:|:---:|:---:|:-----:|\n",
       "| ATG...TAA | 563.0 | 0.767 | 0.413 | 1.0 | 0.47 | 3 min |  0  |  0  |  0  |  3  |  1  |  1  | 0.009 |"
      ],
      "text/plain": [
       "+-----------+-------+-------+-------+-----+------+-------+-----+-----+-----+-----+-----+-----+-------+\n",
       "|    cds    |  len  |  cai  |   gc  | sta | stp  | n-end | CGA | CGG | CGC | CCG | CTC | GCG |  rare |\n",
       "+-----------+-------+-------+-------+-----+------+-------+-----+-----+-----+-----+-----+-----+-------+\n",
       "| ATG...TAA | 563.0 | 0.767 | 0.413 | 1.0 | 0.47 | 3 min |  0  |  0  |  0  |  3  |  1  |  1  | 0.009 |\n",
       "+-----------+-------+-------+-------+-----+------+-------+-----+-----+-----+-----+-----+-----+-------+"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "genes = []\n",
    "for orf in orfs:\n",
    "    display_markdown(f\"# {orf.id}\", raw=True)\n",
    "    assert orf.useguid() in orf.description\n",
    "    assert orf.isorf()\n",
    "    display(orf.express())\n",
    "    hit, *rest_of_hits = genbank_accession(str(orf.seq))\n",
    "    item, start, stop = hit\n",
    "    genes.append(GenbankRecord(orf, item=item, start=start, stop=stop, strand=1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[Gbnk(-1578 CP072089 1046219-1047796), Gbnk(-1689 CP046087 678143-679831)]"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "#pathway_name = \"pTA1_ENO2_CTT1_FBA1\"\n",
    "pathway_name = \"pTA1_ENO2_CTT1_FBA1_ATF1_PGI1\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['pTA1', 'ENO2', 'CTT1', 'FBA1', 'ATF1', 'PGI1']"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "items = [n.strip().split(\"tp\",1)[0] for n in pathway_name.split(\"_\")]\n",
    "items"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "backbone_vector, *elements = items"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "assert os.path.exists(sequence_library_path/f\"{backbone_vector}.gb\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ENO2', 'CTT1', 'FBA1', 'ATF1', 'PGI1']"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "elements"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "promoters, genes, terminators = elements[0:-1:2], elements[1::2], elements[2::2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "promoter(s) ['ENO2', 'FBA1']\n",
      "gene(s) ['CTT1', 'ATF1']\n",
      "terminator(s) ['FBA1', 'PGI1']\n"
     ]
    }
   ],
   "source": [
    "print(\"promoter(s)\", promoters)\n",
    "print(\"gene(s)\", genes)\n",
    "print(\"terminator(s)\", terminators)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pTA1_ENO2_CTT1_FBA1.gb\n",
      "pTA1_FBA1_ATF1_PGI1.gb\n"
     ]
    }
   ],
   "source": [
    "cassette_vector_paths = []\n",
    "for p, g, t in zip(promoters, genes, terminators):\n",
    "    cassette_vector_path = Path( f\"{backbone_vector}_{p}_{g}_{t}.gb\" )\n",
    "    print(cassette_vector_path.name)\n",
    "    cassette_vector_paths.append(cassette_vector_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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