DIMPLE.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "view-in-github"
   },
   "source": [
    "<a href=\"https://colab.research.google.com/github/coywil26/DIMPLE/blob/master/DIMPLE.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "cellView": "form",
    "id": "FHy8rovTWDVB"
   },
   "outputs": [],
   "source": [
    "#@title 1. Install\n",
    "\n",
    "#@markdown Please execute each cell by pressing the *Play* button on the left.\n",
    "\n",
    "# download github \"https://github.com/coywil26/DIMPLE\" and install dependencies\n",
    "!git clone https://github.com/coywil26/DIMPLE\n",
    "\n",
    "!pip install -r DIMPLE/requirements.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "cellView": "form",
    "id": "dbA01B3wWfMP"
   },
   "outputs": [],
   "source": [
    "#@title 2. Upload target file\n",
    "#@markdown Please execute to upload file\n",
    "from google.colab import files\n",
    "\n",
    "uploaded = files.upload()\n",
    "\n",
    "for fn in uploaded.keys():\n",
    "  print('User uploaded file \"{name}\" with length {length} bytes'.format(\n",
    "      name=fn, length=len(uploaded[fn])))\n",
    "target_file = fn\n",
    "!mkdir workspace\n",
    "!mv $target_file workspace\n",
    "directory = \"workspace/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "cellView": "form",
    "id": "J-ZYosDxWqZR"
   },
   "outputs": [],
   "source": [
    "#@title 3. Generate Mutation Fragments and Primers\n",
    "#@markdown Oligo Parameters\n",
    "from google.colab import files\n",
    "import os\n",
    "import argparse\n",
    "from DIMPLE.DIMPLE.DIMPLE import align_genevariation, print_all, post_qc, addgene, DIMPLE, generate_DMS_fragments\n",
    "from DIMPLE.DIMPLE.utilities import parse_custom_mutations, codon_usage\n",
    "from Bio.Seq import Seq\n",
    "from google.colab import data_table\n",
    "import ast\n",
    "import pandas as pd\n",
    "\n",
    "class arguments:\n",
    "  pass\n",
    "args = arguments()\n",
    "\n",
    "# if target_file doesnt exist use default test file\n",
    "if 'target_file' not in locals():\n",
    "  target_file = \"DIMPLE/tests/combined_fasta.fa\"\n",
    "  args.wDir = \"DIMPLE/tests/\"\n",
    "  print('test run')\n",
    "else:\n",
    "  #args.wDir = os.path.basename(target_file)\n",
    "  args.wDir = directory\n",
    "\n",
    "args.geneFile = target_file\n",
    "\n",
    "args.oligoLen = 250 #@param {type:\"integer\"}\n",
    "args.fragmentLen = \"auto\"  #@param {type:\"string\"}\n",
    "if args.fragmentLen == \"auto\":\n",
    "  args.fragmentLen = \"\"\n",
    "args.overlap = 4 #@param {type:\"integer\"}\n",
    "args.barcode_start = 0 #@param {type:\"integer\"}\n",
    "type_IIS_restriction_enzyme = \"BsmBI\" #@param [\"BsmBI\", \"BsaI\"]\n",
    "if type_IIS_restriction_enzyme == \"BsmBI\":\n",
    "  args.restriction_sequence = \"CGTCTC\"\n",
    "else:\n",
    "  args.restriction_sequence = \"GGTCTC\"\n",
    "sequences_to_avoid = \"CGTCTC, GGTCTC\" #@param {type:\"string\"}\n",
    "args.avoid_sequence = sequences_to_avoid.split(\", \")\n",
    "args.matchSequences = False\n",
    "\n",
    "#@markdown Codon Usage (If using custom usage you will see a button to upload file at the bottom)\n",
    "args.usage = \"human\" #@param [\"human\", \"ecoli\"]\n",
    "custom_codon_usage = False #@param {type:\"boolean\"}\n",
    "# input custom mutation file\n",
    "if custom_codon_usage:\n",
    "  print(\"Look in DIMPLE/data/custom_codon_usage.txt for example file\")\n",
    "  uploaded = files.upload()\n",
    "  usage_file = list(uploaded.keys())[0]\n",
    "  with open(usage_file) as f:\n",
    "    usage = f.readlines()\n",
    "  args.usage = ast.literal_eval(usage[0].strip('\\n'))\n",
    "  pd.DataFrame(args.usage,index=[0])\n",
    "\n",
    "#@markdown Select Mutations\n",
    "select_domain_insertion = False #@param {type:\"boolean\"}\n",
    "if select_domain_insertion:\n",
    "  args.dis = True\n",
    "else:\n",
    "  args.dis = False\n",
    "args.handle = \"AGCGGGAGACCGGGGTCTCTGAGC\" #@param {type:\"string\"}\n",
    "select_insertions = False #@param {type:\"boolean\"}\n",
    "insertions = \"GGG,GGGGGG\" #@param {type:\"string\"}\n",
    "if select_insertions:\n",
    "  args.insertions = insertions.split(\",\")\n",
    "else:\n",
    "  args.insertions = \"\"\n",
    "select_deletions = False #@param {type:\"boolean\"}\n",
    "deletions = \"3,6\" #@param {type:\"string\"}\n",
    "if select_deletions:\n",
    "  args.deletions = deletions.split(\",\")\n",
    "else:\n",
    "  args.deletions = \"\"\n",
    "select_deep_mutation_scan = False #@param {type:\"boolean\"}\n",
    "if select_deep_mutation_scan:\n",
    "  args.dms = True\n",
    "else:\n",
    "  args.dms = False\n",
    "amino_acid_substitutions = \"Cys,Asp,Ser,Gln,Met,Asn,Pro,Lys,Thr,Phe,Ala,Gly,Ile,Leu,His,Arg,Trp,Val,Glu,Tyr\" #@param {type:\"string\"}\n",
    "args.include_stop_codons = False #@param {type:\"boolean\"}\n",
    "args.include_synonymous_mutations = False #@param {type:\"boolean\"}\n",
    "select_custom_mutations = False #@param {type:\"boolean\"}\n",
    "if select_custom_mutations:\n",
    "  print(\"Look in DIMPLE/data/custom_codon_usage.txt for example file\")\n",
    "  uploaded = files.upload()\n",
    "  custom_mutations_file = list(uploaded.keys())[0]\n",
    "  with open(custom_mutations_file) as f:\n",
    "    lines = f.readlines()\n",
    "  args.custom_mutations = parse_custom_mutations(lines[1:])\n",
    "  pd.DataFrame(args.custom_mutations,index=[0])\n",
    "else:\n",
    "  args.custom_mutations = {}\n",
    "args.make_double_mutations = False #@param {type:\"boolean\"}\n",
    "\n",
    "#!python3 DIMPLE/run_dimple.py -geneFile=$target_file -oligoLen=$oligo_length -DMS=$select_DMS -usage=$codon_usage_bias -include_stop_codons=$include_stop_codons -restriction_sequence=$type_IIS_restriction_enzyme -avoid_sequence=$sequences_to_avoid -insertions=$insertions -deletions=$deletions -fragmentLen=$fragment_length -overlap=$fragment_overlap -barcode_start=$barcode_start_position -include_stop_codons=$include_stop_codons -usage=$custom_mutations\n",
    "\n",
    "\n",
    "# Check genetic handle for non nucleic characters\n",
    "if any([x not in ['A', 'C', 'G', 'T', 'a', 'c', 'g', 't'] for x in args.handle]):\n",
    "    raise ValueError('Genetic handle contains non nucleic bases')\n",
    "\n",
    "#DIMPLE.handle = args.handle\n",
    "DIMPLE.synth_len = args.oligoLen\n",
    "if args.fragmentLen:\n",
    "    DIMPLE.maxfrag = args.fragmentLen\n",
    "else:\n",
    "    DIMPLE.maxfrag = args.oligoLen - 62 - args.overlap  # 62 allows for cutsites and barcodes\n",
    "\n",
    "DIMPLE.dms = args.dms\n",
    "\n",
    "#  adjust primer primerBuffer\n",
    "DIMPLE.primerBuffer += args.overlap\n",
    "\n",
    "DIMPLE.avoid_sequence = args.avoid_sequence\n",
    "DIMPLE.barcodeF = DIMPLE.barcodeF[int(args.barcode_start):]\n",
    "DIMPLE.barcodeR = DIMPLE.barcodeR[int(args.barcode_start):]\n",
    "DIMPLE.cutsite = Seq(args.restriction_sequence)\n",
    "DIMPLE.avoid_sequence = [Seq(x) for x in args.avoid_sequence]\n",
    "DIMPLE.stop_codon = args.include_stop_codons\n",
    "DIMPLE.make_double = args.make_double_mutations\n",
    "DIMPLE.usage = codon_usage(args.usage)\n",
    "\n",
    "OLS = addgene(os.path.join(args.wDir, args.geneFile).strip())\n",
    "\n",
    "if args.matchSequences == 'match':\n",
    "    align_genevariation(OLS)\n",
    "if args.deletions:\n",
    "    args.deletions = [int(x) for x in args.deletions]\n",
    "if not any([args.dms, args.insertions, args.deletions]):\n",
    "    raise ValueError(\"Didn't select any mutations to generate\")\n",
    "print(args.dms)\n",
    "print(args.overlap)\n",
    "generate_DMS_fragments(OLS, args.overlap, args.overlap, args.include_synonymous_mutations, args.custom_mutations, args.dms, args.insertions, args.deletions, args.dis, args.wDir)\n",
    "\n",
    "post_qc(OLS)\n",
    "print_all(OLS, args.wDir)\n",
    "\n",
    "directory = args.wDir\n",
    "!zip -r file.zip $directory\n",
    "files.download(\"file.zip\")"
   ]
  }
 ],
 "metadata": {
  "colab": {
   "authorship_tag": "ABX9TyMMNXDUaQ6ReB+IW1kJN6kT",
   "include_colab_link": true,
   "provenance": []
  },
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.10.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}