sequence_network.ipynb

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   "cell_type": "markdown",
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   "source": [
    "# Visualizing the sequence space around *Tk*MAT\n",
    "\n",
    "In the followng example, the sequence spece of the methionine adenosyltransferase from *Thermococcus kodakarensis* (\"WP_011249500.1\") is visualized. This includes the following steps:\n",
    "1. Get the *Tk*MAT sequence and all annotated information based on the accession ID\n",
    "2. 200 similare sequences are retrieved with annotations based on a BLAST search\n",
    "3. A pairwise alignment is performed between all unique sequence pairs\n",
    "4. A sequence network is constructed based on the sequence similarity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Notebook setup\n",
    "import sys\n",
    "\n",
    "IN_COLAB = 'google.colab' in sys.modules\n",
    "\n",
    "if IN_COLAB:\n",
    "    !git clone https://github.com/PyEED/colab-example.git\n",
    "    %cd colab-example\n",
    "    !pip install  -q -r requirements.txt\n",
    "    %reset -f\n",
    "\n",
    "from pyeed.core import ProteinInfo, Alignment\n",
    "from pyeed.aligners import PairwiseAligner\n",
    "from pyeed.network import SequenceNetwork"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Get a start sequence\n",
    "\n",
    "In the following cell, the methionine adenosyltransferase from *Thermococcus kodakarensis* (metTK) is used as a start sequence. All information of the sequence is retrieved from the NCBI database by passing the accession ID to the `ProteinInfo.from_ncbi()` method. Besides the sequence, all annotation are mapped to the corresponding positions in the [PyEED data model](https://github.com/PyEED/pyeed/blob/main/specifications/data_model.md)."
   ]
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   "cell_type": "code",
   "execution_count": 2,
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[4mProteinInfo\u001b[0m\n",
      "├── \u001b[94mid\u001b[0m = proteininfo0\n",
      "├── \u001b[94msource_id\u001b[0m = WP_011249500.1\n",
      "├── \u001b[94mname\u001b[0m = methionine adenosyltransferase\n",
      "├── \u001b[94msequence\u001b[0m = MAGKVRNIVVEELVRTPVEMQKVELVERKGIGHPDSIADGIAEAVSRALSREYVKRYGIILHHNTDQVEVVGGRAYPQFGGGEVIKPIYILLSGRAVEMVDREFFPVHEIALKAAKDYLRKAVRHLDLEHHVIIDSRIGQGSVDLVGVFNKAKKNPIPLANDTSFGVGYAPLSETEKIVLETEKYLNSDEFKKKYPAVGEDIKVMGLRKGDEIDLTIAAAIVDSEVDNPDDYMAVKEAIYEAAKGIVESHTERPTNIYVNTADDPKEGIYYITVTGTSAEAGDDGSVGRGNRVNGLITPNRHMSMEAAAGKNPVSHVGKIYNILSMLIANDIAEQVEGVEEVYVRILSQIGKPIDEPLVASVQIIPKKGYSIDVLQKPAYEIADEWLANITKIQKMILEDKVNVF\n",
      "├── \u001b[94morganism\u001b[0m\n",
      "│   └── \u001b[4mOrganism\u001b[0m\n",
      "│       ├── \u001b[94mid\u001b[0m = organism0\n",
      "│       ├── \u001b[94mname\u001b[0m = Thermococcus kodakarensis\n",
      "│       ├── \u001b[94mtaxonomy_id\u001b[0m = taxon:311400\n",
      "│       ├── \u001b[94mdomain\u001b[0m = Archaea\n",
      "│       ├── \u001b[94mkingdom\u001b[0m = Euryarchaeota\n",
      "│       ├── \u001b[94mphylum\u001b[0m = Thermococcales\n",
      "│       ├── \u001b[94mtax_class\u001b[0m = Thermococcus\n",
      "│       └── \u001b[94mspecies\u001b[0m = kodakarensis\n",
      "├── \u001b[94mcitation\u001b[0m\n",
      "│   └── \u001b[4mCitation\u001b[0m\n",
      "│       └── \u001b[94mid\u001b[0m = citation0\n",
      "├── \u001b[94mregions\u001b[0m\n",
      "│   └── 0\n",
      "│       └── \u001b[4mProteinRegion\u001b[0m\n",
      "│           ├── \u001b[94mid\u001b[0m = proteinregion0\n",
      "│           ├── \u001b[94mname\u001b[0m = PRK04439\n",
      "│           ├── \u001b[94mspans\u001b[0m\n",
      "│           │   └── 0\n",
      "│           │       └── \u001b[4mSpan\u001b[0m\n",
      "│           │           ├── \u001b[94mid\u001b[0m = span0\n",
      "│           │           ├── \u001b[94mstart\u001b[0m = 5\n",
      "│           │           └── \u001b[94mend\u001b[0m = 405\n",
      "│           ├── \u001b[94mnote\u001b[0m = methionine adenosyltransferase\n",
      "│           └── \u001b[94mcross_reference\u001b[0m = CDD:235298\n",
      "├── \u001b[94mec_number\u001b[0m = 2.5.1.6\n",
      "└── \u001b[94mmol_weight\u001b[0m = 44484.0\n",
      "\n"
     ]
    }
   ],
   "source": [
    "tkMAT = ProteinInfo.from_ncbi(\"WP_011249500.1\")\n",
    "print(tkMAT)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. Make a BLAST search\n",
    "\n",
    "The sequence is used to perform a BLAST search against the NCBI non-redundant protein sequences database. For each hit in the blast search, again all information os retrieved from the NCBI database and mapped to the PyEED data model."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "🏃🏼‍♀️ Running PBLAST\n",
      "╭── protein name: methionine adenosyltransferase\n",
      "├── accession: WP_011249500.1\n",
      "├── organism: Thermococcus kodakarensis\n",
      "├── e-value: 10.0\n",
      "╰── max hits: 200\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "⬇️ Fetching protein sequences: 100%|██████████| 200/200 [00:44<00:00,  4.50it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "🎉 Done\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    }
   ],
   "source": [
    "# Run online blastp search\n",
    "blast_results = tkMAT.ncbi_blastp(n_hits=200)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Create pairwise alignments between all sequences of the blast serach\n",
    "\n",
    "Pairwise alignments are created between all sequences of the blast search. In this Process `PairwiseAlignment` objects are create harbouring information on the identity number of gaps, mismatches, and the alignment score. The identity of each pair is used in the next step to create a sequence network."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "⛓️ Running pairwise alignments: 100%|██████████| 19900/19900 [00:05<00:00, 3704.76it/s]\n"
     ]
    }
   ],
   "source": [
    "# Create pairwise alignments for all combinations\n",
    "multi_parwise_alignments = Alignment.from_sequences(\n",
    "    blast_results, aligner=PairwiseAligner\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4. Create a sequence network\n",
    "\n",
    "A `SequenceNetwork` is created from the pairwise alignments. The network is a graph where each node represents a sequence and each edge represents a pairwise alignment. The identity of the alignment is used as the weight of the edge. The network is then visualized by calling the `visualize()` method."
   ]
  },
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   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
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   "source": [
    "# Create a 3D sequence network based on the indentiy of the pairwise alignments\n",
    "n = SequenceNetwork(\n",
    "    sequences=blast_results,\n",
    "    pairwise_alignments=multi_parwise_alignments,\n",
    "    threshold=0.9,\n",
    "    weight=\"identity\",\n",
    "    dimensions=3,\n",
    "    color=\"taxonomy_id\",\n",
    ")\n",
    "# Mark the query sequence metTK\n",
    "n.add_target(tkMAT)\n",
    "\n",
    "# Visualize the network\n",
    "n.visualize()"
   ]
  }
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