Standardizing and annotating models/Convert model in text file to SBML-qual.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "be983430-e402-4777-9cc8-dc081dcb7672",
   "metadata": {},
   "outputs": [],
   "source": [
    "import biolqm\n",
    "import ginsim\n",
    "import os\n",
    "from rpy2.robjects.packages import importr\n",
    "boolnet = importr(\"BoolNet\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "93e4e6ac-61a2-4743-9450-d886602e43b8",
   "metadata": {},
   "source": [
    "# Standardization\n",
    "\n",
    "## Overview\n",
    "\n",
    "This Jupyter notebook provides tools for converting network in text files to SBML-qual format.  \n",
    "It provides two functions: convert single network and convert multiple networks in a folder.\n",
    "\n",
    "## Usage - single model\n",
    "\n",
    "1. **Input format:** Similar to the Python package `Boolnet`, as described [here](https://rdrr.io/cran/BoolNet/man/loadNetwork.html).\n",
    "2. **Save to File:** Use the `to_SBML` function to save the network to a SBML-qual file.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "5533cd18-5ab6-4575-b3dd-4c5474f6a3a3",
   "metadata": {},
   "outputs": [],
   "source": [
    "home = \"persistent/\" # home path for Logic Model Merger\n",
    "model_name = \"Bonzanni2013\"\n",
    "txt_file = home + \"LogicModelMerger/Models/\" + model_name + \".txt\"\n",
    "sbml_file = home + \"LogicModelMerger/Models/\" + model_name + \".sbml\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "0bb4b15b-cedf-4cbb-a78f-cb166fea3b2e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Boolean network with 11 genes\n",
      "\n",
      "Involved genes:\n",
      "SPI1 GATA1 GATA2 TAL1 ZFPM1 FLI1 ERG CBFA2T3 RUNX1 SMAD6 HHEX\n",
      "\n",
      "Transition functions:\n",
      "SPI1 = ((FLI1 | RUNX1 | SPI1) & !(SPI1 & GATA1))\n",
      "GATA1 = ((TAL1 & GATA1) & !(SPI1 & GATA1))\n",
      "GATA2 = ((FLI1 | ERG | (TAL1 & GATA2)) & !(GATA1 & ZFPM1) & !(GATA2 & HHEX))\n",
      "TAL1 = (FLI1 | ERG | (FLI1 & GATA2) | (TAL1 & GATA1) | (GATA2 & TAL1))\n",
      "ZFPM1 = (GATA2 & TAL1)\n",
      "FLI1 = ((FLI1 | GATA2 | ERG | (GATA2 & TAL1)) & !GATA1)\n",
      "ERG = ((FLI1 | ERG | GATA2 | RUNX1) & !(TAL1 & CBFA2T3))\n",
      "CBFA2T3 = (TAL1 & GATA2)\n",
      "RUNX1 = ((SPI1 | RUNX1 | FLI1 | ERG | (GATA2 & TAL1)) & !(RUNX1 & SMAD6))\n",
      "SMAD6 = (ERG | FLI1 | (TAL1 & GATA2))\n",
      "HHEX = (FLI1 | ERG | (TAL1 & GATA2))\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Load the network in text file\n",
    "net = boolnet.loadNetwork(txt_file)\n",
    "\n",
    "# Export to SBML\n",
    "boolnet.toSBML(net, sbml_file)\n",
    "print(boolnet.loadSBML(sbml_file))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "e227e635-ab81-404f-9780-21f4f0069603",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<img class=\"unconfined\" width=\"369px\" src=\"data:image/svg+xml;base64,<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20001102//EN" "http://www.w3.org/TR/2000/CR-SVG-20001102/DTD/svg-20001102.dtd">
<svg width="369.0" height="364.0" xmlns="http://www.w3.org/2000/svg" version="1.1">
  <style type="text/css">
text {
  font-family: 'SansSerif';
  font-size: 12px;
}
.node .shape {
fill: #ffffff;
stroke: #000000;
}
.node text {
fill: #000000;
}
.edge {
stroke: #000000;
fill: none;
stroke-width: 1;
}
.edge_POSITIVE {
stroke: #00c800;
}
.edge_NEGATIVE {
stroke: #c80000;
}
.edge_DUAL {
stroke: #0000c8;
}
</style>
  <defs>
    <marker id="Marker_DUAL_0000c8" viewBox="-7 -7 12 15" orient="auto" markerHeight="9" markerWidth="9">
      <path stroke="#0000c8" fill="#0000c8" d="M -6 -5 L -6 5 L -5 5 L -5 0 L -2 0 L -4 5 L 2 0 L -4 -5 L -2 0 L -5 0 L -5 -5 z"/>
    </marker>
  </defs>
  <path class="edge edge_DUAL" marker-end="url(#Marker_DUAL_0000c8)" d="M 206.0 153.0 L 206.0 138.0 L 233.0 138.0 L 233.0 165.0 L 221.0 165.0"/>
  <defs>
    <marker id="Marker_POSITIVE_00c800" viewBox="-7 -7 12 15" orient="auto" markerHeight="9" markerWidth="9">
      <path stroke="#00c800" fill="#00c800" d="M -4 -5 L -2 0 L -4 5 L 2 0 z"/>
    </marker>
  </defs>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 220.0 156.0 L 220.0 156.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 171.0 151.0 L 123.0 144.0 L 120.0 130.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 220.0 180.0 L 232.0 202.0 L 232.0 215.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 220.0 151.0 L 265.0 129.0 L 280.0 129.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 203.0 151.0 L 266.0 55.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 209.0 180.0 L 282.0 241.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 220.0 170.0 L 315.0 192.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 180.0 151.0 L 180.0 109.0 L 180.0 96.0"/>
  <defs>
    <marker id="Marker_NEGATIVE_c80000" viewBox="-7 -7 12 15" orient="auto" markerHeight="9" markerWidth="9">
      <path stroke="#c80000" fill="#c80000" d="M -1 -4 L -1 4 L 1 4 L 1 -4 z"/>
    </marker>
  </defs>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 120.0 129.0 L 167.0 135.0 L 170.0 149.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 273.0 272.0 L 258.0 324.0 L 248.0 330.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 289.0 243.0 L 289.0 172.0 L 289.0 146.0"/>
  <path class="edge edge_DUAL" marker-end="url(#Marker_DUAL_0000c8)" d="M 308.0 245.0 L 308.0 230.0 L 335.0 230.0 L 335.0 257.0 L 323.0 257.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 282.0 145.0 L 236.0 166.0 L 221.0 166.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 282.0 145.0 L 263.0 156.0 L 261.0 156.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 282.0 145.0 L 270.0 204.0 L 258.0 215.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 317.0 118.0 L 317.0 103.0 L 344.0 103.0 L 344.0 130.0 L 332.0 130.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 314.0 145.0 L 314.0 215.0 L 314.0 241.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 312.0 145.0 L 333.0 181.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 282.0 120.0 L 221.0 90.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 279.0 54.0 L 302.0 114.0"/>
  <path class="edge edge_DUAL" marker-end="url(#Marker_DUAL_0000c8)" d="M 233.0 334.0 L 233.0 319.0 L 260.0 319.0 L 260.0 346.0 L 248.0 346.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 198.0 332.0 L 160.0 300.0 L 160.0 278.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 247.0 332.0 L 261.0 279.0 L 271.0 273.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 227.0 244.0 L 227.0 333.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 208.0 217.0 L 195.0 194.0 L 195.0 181.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 233.0 219.0 L 233.0 164.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 243.0 219.0 L 243.0 204.0 L 270.0 204.0 L 270.0 231.0 L 258.0 231.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 257.0 217.0 L 268.0 157.0 L 280.0 146.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 257.0 240.0 L 271.0 247.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 257.0 224.0 L 315.0 204.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 229.0 217.0 L 198.0 96.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 332.0 212.0 L 307.0 241.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 210.0 95.0 L 210.0 136.0 L 210.0 149.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 211.0 165.0 L 184.0 233.0 L 168.0 246.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 211.0 158.0 L 211.0 158.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 246.0 138.0 L 246.0 123.0 L 273.0 123.0 L 273.0 150.0 L 261.0 150.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 211.0 144.0 L 121.0 120.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 260.0 136.0 L 278.0 124.0 L 280.0 124.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 239.0 136.0 L 270.0 55.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 242.0 165.0 L 289.0 241.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 260.0 160.0 L 315.0 187.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 228.0 136.0 L 203.0 96.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 167.0 277.0 L 204.0 308.0 L 204.0 330.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 153.0 250.0 L 153.0 235.0 L 180.0 235.0 L 180.0 262.0 L 168.0 262.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 149.0 248.0 L 188.0 181.0"/>
  <path class="edge edge_POSITIVE" marker-end="url(#Marker_POSITIVE_00c800)" d="M 167.0 248.0 L 193.0 179.0 L 209.0 166.0"/>
  <path class="edge edge_NEGATIVE" marker-end="url(#Marker_NEGATIVE_c80000)" d="M 167.0 254.0 L 206.0 239.0"/>
  <g id="SPI1" class="node">
    <ellipse id="SPI1_shape" class="shape" cx="222.5" cy="346.5" rx="22.5" ry="12.5"/>
    <text  id="SPI1_text" x="222" y="349" text-anchor="middle">SPI1</text>
  </g>
  <g id="GATA1" class="node">
    <ellipse id="GATA1_shape" class="shape" cx="142.5" cy="262.5" rx="22.5" ry="12.5"/>
    <text  id="GATA1_text" x="142" y="265" text-anchor="middle">GATA1</text>
  </g>
  <g id="GATA2" class="node">
    <ellipse id="GATA2_shape" class="shape" cx="195.5" cy="165.5" rx="22.5" ry="12.5"/>
    <text  id="GATA2_text" x="195" y="168" text-anchor="middle">GATA2</text>
  </g>
  <g id="TAL1" class="node">
    <ellipse id="TAL1_shape" class="shape" cx="235.5" cy="150.5" rx="22.5" ry="12.5"/>
    <text  id="TAL1_text" x="235" y="153" text-anchor="middle">TAL1</text>
  </g>
  <g id="ZFPM1" class="node">
    <ellipse id="ZFPM1_shape" class="shape" cx="95.5" cy="114.5" rx="22.5" ry="12.5"/>
    <text  id="ZFPM1_text" x="95" y="117" text-anchor="middle">ZFPM1</text>
  </g>
  <g id="FLI1" class="node">
    <ellipse id="FLI1_shape" class="shape" cx="232.5" cy="231.5" rx="22.5" ry="12.5"/>
    <text  id="FLI1_text" x="232" y="234" text-anchor="middle">FLI1</text>
  </g>
  <g id="ERG" class="node">
    <ellipse id="ERG_shape" class="shape" cx="306.5" cy="130.5" rx="22.5" ry="12.5"/>
    <text  id="ERG_text" x="306" y="133" text-anchor="middle">ERG</text>
  </g>
  <g id="CBFA2T3" class="node">
    <ellipse id="CBFA2T3_shape" class="shape" cx="275.5" cy="39.5" rx="22.5" ry="12.5"/>
    <text  id="CBFA2T3_text" x="275" y="42" text-anchor="middle">CBFA2T3</text>
  </g>
  <g id="RUNX1" class="node">
    <ellipse id="RUNX1_shape" class="shape" cx="297.5" cy="257.5" rx="22.5" ry="12.5"/>
    <text  id="RUNX1_text" x="297" y="260" text-anchor="middle">RUNX1</text>
  </g>
  <g id="SMAD6" class="node">
    <ellipse id="SMAD6_shape" class="shape" cx="341.5" cy="197.5" rx="22.5" ry="12.5"/>
    <text  id="SMAD6_text" x="341" y="200" text-anchor="middle">SMAD6</text>
  </g>
  <g id="HHEX" class="node">
    <ellipse id="HHEX_shape" class="shape" cx="195.5" cy="80.5" rx="22.5" ry="12.5"/>
    <text  id="HHEX_text" x="195" y="83" text-anchor="middle">HHEX</text>
  </g>
</svg>
\">"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Visulize the network\n",
    "lqm = biolqm.load(sbml_file)\n",
    "lrg = biolqm.to_ginsim(lqm)\n",
    "ginsim.show(lrg)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c117a2b2",
   "metadata": {},
   "source": [
    "## Usage - multiple models\n",
    "\n",
    "1. **Input format:** A folder containing text files with the network in the same format as the Python package `Boolnet`, as described [here](https://rdrr.io/cran/BoolNet/man/loadNetwork.html).\n",
    "2. **Save to File:** Use the `to_SBML` function to save the network to a SBML-qual file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "4037f46a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of models converted: 3\n"
     ]
    }
   ],
   "source": [
    "folder_path = home + \"LogicModelMerger/Models/\"\n",
    "num_models_converted = 0\n",
    "for file in os.listdir(folder_path):\n",
    "    if file.endswith(\".txt\"):\n",
    "        model_name = file.split(\".\")[0]\n",
    "        sbml_file = folder_path + model_name + \".sbml\"\n",
    "        net = boolnet.loadNetwork(folder_path + file)\n",
    "        try:\n",
    "            boolnet.toSBML(net, sbml_file)\n",
    "            num_models_converted += 1\n",
    "        except:\n",
    "            print(f\"Error converting {file}\")\n",
    "#Print the number of models converted\n",
    "print(f\"Number of models converted: {num_models_converted}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "99e2f4be",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Inspecting one model: persistent/Models/Updated/merged_and_Bonzanni2013_Krumsiek2011.sbml\n",
      "Boolean network with 18 genes\n",
      "\n",
      "Involved genes:\n",
      "ERG CBFA2T3 RUNX1 SMAD6 HHEX KLF1 CEBPA JUN EGR1 EGR2 NAB1 GFI1 GATA1 GATA2 ZFPM1 TAL1 SPI1 FLI1\n",
      "\n",
      "Transition functions:\n",
      "ERG = ((FLI1 | ERG | GATA2 | RUNX1) & !(TAL1 & CBFA2T3))\n",
      "CBFA2T3 = (TAL1 & GATA2)\n",
      "RUNX1 = ((SPI1 | RUNX1 | FLI1 | ERG | (GATA2 & TAL1)) & !(RUNX1 & SMAD6))\n",
      "SMAD6 = (ERG | FLI1 | (TAL1 & GATA2))\n",
      "HHEX = (FLI1 | ERG | (TAL1 & GATA2))\n",
      "KLF1 = (GATA1 & !FLI1)\n",
      "CEBPA = (CEBPA & !(GATA1 & ZFPM1 & TAL1))\n",
      "JUN = (SPI1 & !GFI1)\n",
      "EGR1 = ((SPI1 & JUN) & !GFI1)\n",
      "EGR2 = ((SPI1 & JUN) & !GFI1)\n",
      "NAB1 = ((SPI1 & JUN) & !GFI1)\n",
      "GFI1 = (CEBPA & !(EGR1 | EGR2 | NAB1))\n",
      "GATA1 = ((TAL1 & GATA1) & !(SPI1 & GATA1) & (GATA1 | GATA2 | FLI1) & !SPI1)\n",
      "GATA2 = ((FLI1 | ERG | (TAL1 & GATA2)) & !(GATA1 & ZFPM1) & !(GATA2 & HHEX) & GATA2 & !(GATA1 & ZFPM1) & SPI1)\n",
      "ZFPM1 = (GATA2 & TAL1 & GATA1)\n",
      "TAL1 = ((FLI1 | ERG | (FLI1 & GATA2) | (TAL1 & GATA1) | (GATA2 & TAL1)) & GATA1 & !SPI1)\n",
      "SPI1 = ((FLI1 | RUNX1 | SPI1) & !(SPI1 & GATA1) & (CEBPA | SPI1) & !(GATA1 | GATA2))\n",
      "FLI1 = ((FLI1 | GATA2 | ERG | (GATA2 & TAL1)) & !GATA1 & GATA1 & !KLF1)\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(f\"Inspecting one model: {sbml_file}\")\n",
    "print(boolnet.loadSBML(sbml_file))"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}