evaluate_carbon_usage.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "b9f12997-d805-4be4-8333-c6ed72c43ad8",
   "metadata": {},
   "outputs": [],
   "source": [
    "# loading necessary packages\n",
    "import cobra\n",
    "from cobra import Model, Reaction, Metabolite\n",
    "from cobra.io import load_model\n",
    "from cobra.io import read_sbml_model\n",
    "from cobra.medium import minimal_medium\n",
    "import pandas as pd\n",
    "import copy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "aa49a5db-ac2d-4234-a172-f73db9874865",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_path = \"/projectnb2/talbot-lab-data/zrwerbin/soil_microbe_GEMs/iAA1300/iAA1300_modified_cobra.xml\"\n",
    "modelID = \"iAA1300/iAA1300_modified_cobra.xml\"\n",
    "project_dir = \"/projectnb2/talbot-lab-data/zrwerbin/soil_microbe_GEMs/\"\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "d6127878-99e4-4528-9b9f-5c1b00013104",
   "metadata": {},
   "outputs": [],
   "source": [
    "major_carbon_sources={\"MNXM726888_e\":0, \"MNXM1105810_e\":0, \"MNXM1137670_e\":0, \"MNXM1106000_e\":0, \"MNXM1104432_e\":0, \"MNXM1108175_e\":0}\n",
    "minor_carbon_sources={\"MNXM726888_e\":0, \"MNXM738068_e\":0, \"MNXM1105810_e\":0, \"MNXM1137670_e\":0, \"MNXM1107769_e\":0, \"MNXM1106000_e\":0, \"MNXM1105732_e\":0, \"MNXM739527_e\":0, \"MNXM1107821_e\":0, \"MNXM1108206_e\":0, \"MNXM37_e\":0, \"MNXM741173_e\":0, \"MNXM29_e\":0, \"MNXM728337_e\":0, \"MNXM1106762_e\":0, \"MNXM1106164_e\":0, \"MNXM738804_e\":0, \"MNXM741664_e\":0, \"MNXM114_e\":0, \"MNXM737787_e\":0, \"MNXM142_e\":0, \"MNXM741553_e\":0, \"MNXM76_e\":0, \"MNXM199_e\":0, \"MNXM1104432_e\":0, \"MNXM1108175_e\":0}\n",
    "M8_media={\"MNXM7454_e\":1000, \"MNXM421_e\":1000, \"MNXM26_e\":1000, \"MNXM168_e\":1000, \"MNXM1105732_e\":1000, \"MNXM739527_e\":1000, \"MNXM727871_e\":1000, \"MNXM1107821_e\":1000, \"MNXM1108206_e\":1000, \"MNXM304_e\":1000, \"MNXM458_e\":1000, \"MNXM128_e\":1000, \"MNXM1104756_e\":1000, \"MNXM1104738_e\":1000, \"MNXM726888_e\":1000, \"MNXM1107753_e\":1000, \"MNXM735978_e\":1000, \"MNXM90960_e\":1000, \"MNXM731166_e\":1000, \"MNXM738068_e\":1000, \"MNXM726711_e\":1000, \"MNXM726712_e\":1000, \"MNXM617_e\":1000, \"MNXM1105810_e\":1000, \"MNXM1137670_e\":1000, \"MNXM37_e\":1000, \"MNXM741173_e\":1000, \"MNXM29_e\":1000, \"MNXM490899_e\":1000, \"MNXM733114_e\":1000, \"MNXM1_e\":1000, \"WATER_e\":1000, \"MNXM60_e\":1000, \"MNXM1107769_e\":1000, \"MNXM728337_e\":1000, \"MNXM1105941_e\":1000, \"MNXM95_e\":1000, \"MNXM1104432_e\":1000, \"MNXM1106762_e\":1000, \"MNXM729132_e\":1000, \"MNXM1106164_e\":1000, \"MNXM1106000_e\":1000, \"MNXM738804_e\":1000, \"MNXM653_e\":1000, \"MNXM2255_e\":1000, \"MNXM2397_e\":1000, \"MNXM726092_e\":1000, \"MNXM27_e\":1000, \"MNXM274_e\":1000, \"MNXM8_e\":1000, \"MNXM729302_e\":1000, \"MNXM731950_e\":1000, \"MNXM732398_e\":1000, \"MNXM741664_e\":1000, \"MNXM249_e\":1000, \"MNXM9_e\":1000, \"MNXM734864_e\":1000, \"MNXM1094052_e\":1000, \"MNXM114_e\":1000, \"MNXM548_e\":1000, \"MNXM419_e\":1000, \"MNXM270_e\":1000, \"MNXM737787_e\":1000, \"MNXM1157_e\":1000, \"MNXM58_e\":1000, \"MNXM730135_e\":1000, \"MNXM142_e\":1000, \"MNXM741553_e\":1000, \"MNXM741004_e\":1000, \"MNXM76_e\":1000, \"MNXM158_e\":1000, \"MNXM199_e\":1000, \"MNXM174_e\":1000, \"MNXM729215_e\":1000}\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "6d646529-403e-4945-b8bf-61f491683b40",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'c': '', 'e': '', 'p': '', 'C_e': ''}"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#model.summary()\n",
    "model.compartments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "6d7ac2d6-efa4-4353-94db-c594cb1c1554",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/projectnb2/talbot-lab-data/zrwerbin/soil_microbe_GEMs/iAA1300/iAA1300_modified_cobra.xml\n",
      "iAA1300/iAA1300_modified_cobra.xml\n",
      "/projectnb2/talbot-lab-data/zrwerbin/soil_microbe_GEMs/iAA1300/iAA1300_modified_cobra.xml\n",
      "{'EX_MNXM9_e': 1000.0, 'EX_MNXM1_e': 1000.0, 'EX_MNXM726712_e': 0.05, 'EX_MNXM2255_e': 1000.0, 'EX_MNXM726711_e': 0.05, 'EX_MNXM1137670_e': 5.0, 'EX_MNXM729215_e': 1000.0, 'EX_MNXM653_e': 1000.0, 'EX_MNXM128_e': 1000.0, 'EX_MNXM731950_e': 1000.0, 'EX_MNXM731166_e': 1000.0, 'EX_MNXM90960_e': 1000.0, 'EX_WATER_e': 1000.0, 'EX_nh4_e': 5.0, 'EX_MNXM726092_e': 1000.0, 'EX_MNXM58_e': 1000.0, 'EX_MNXM95_e': 1000.0, 'EX_MNXM735438_e': 1000.0, 'EX_MNXM735978_e': 1000.0, 'EX_MNXM739758_e': 1000.0}\n",
      "MNXM7454_e\n",
      "MNXM421_e\n",
      "MNXM26_e\n",
      "MNXM168_e\n",
      "MNXM1105732_e\n",
      "MNXM739527_e\n",
      "MNXM727871_e\n",
      "MNXM1107821_e\n",
      "MNXM1108206_e\n",
      "MNXM304_e\n",
      "MNXM458_e\n",
      "MNXM1104756_e\n",
      "MNXM1104738_e\n",
      "MNXM726888_e\n",
      "MNXM1107753_e\n",
      "MNXM738068_e\n",
      "MNXM617_e\n",
      "MNXM1105810_e\n",
      "MNXM37_e\n",
      "MNXM741173_e\n",
      "MNXM29_e\n",
      "MNXM490899_e\n",
      "MNXM733114_e\n",
      "MNXM60_e\n",
      "MNXM1107769_e\n",
      "MNXM728337_e\n",
      "MNXM1105941_e\n",
      "MNXM1104432_e\n",
      "MNXM1106762_e\n",
      "MNXM729132_e\n",
      "MNXM1106164_e\n",
      "MNXM1106000_e\n",
      "MNXM738804_e\n",
      "MNXM2397_e\n",
      "MNXM27_e\n",
      "MNXM274_e\n",
      "MNXM8_e\n",
      "MNXM729302_e\n",
      "MNXM732398_e\n",
      "MNXM741664_e\n",
      "MNXM249_e\n",
      "MNXM734864_e\n",
      "MNXM1094052_e\n",
      "MNXM114_e\n",
      "MNXM548_e\n",
      "MNXM419_e\n",
      "MNXM270_e\n",
      "MNXM737787_e\n",
      "MNXM1157_e\n",
      "MNXM730135_e\n",
      "MNXM142_e\n",
      "MNXM741553_e\n",
      "MNXM741004_e\n",
      "MNXM76_e\n",
      "MNXM158_e\n",
      "MNXM199_e\n",
      "MNXM174_e\n",
      "default growth rate:\n",
      "31.591408020625753\n",
      "{'EX_MNXM9_e': 1000, 'EX_MNXM1_e': 1000, 'EX_MNXM726712_e': 1000, 'EX_MNXM2255_e': 1000, 'EX_MNXM726711_e': 1000, 'EX_MNXM1137670_e': 0, 'EX_MNXM729215_e': 1000, 'EX_MNXM653_e': 1000, 'EX_MNXM128_e': 1000, 'EX_MNXM731950_e': 1000, 'EX_MNXM731166_e': 1000, 'EX_MNXM90960_e': 1000, 'EX_WATER_e': 1000, 'EX_nh4_e': 5.0, 'EX_MNXM726092_e': 1000, 'EX_MNXM58_e': 1000, 'EX_MNXM95_e': 1000, 'EX_MNXM735438_e': 1000.0, 'EX_MNXM735978_e': 1000, 'EX_MNXM739758_e': 1000.0, 'EX_MNXM7454_e': 1000, 'EX_MNXM421_e': 1000, 'EX_MNXM26_e': 1000, 'EX_MNXM168_e': 1000, 'EX_MNXM1105732_e': 1000, 'EX_MNXM739527_e': 1000, 'EX_MNXM727871_e': 1000, 'EX_MNXM1107821_e': 1000, 'EX_MNXM1108206_e': 1000, 'EX_MNXM304_e': 1000, 'EX_MNXM458_e': 1000, 'EX_MNXM1104756_e': 1000, 'EX_MNXM1104738_e': 1000, 'EX_MNXM726888_e': 0, 'EX_MNXM1107753_e': 1000, 'EX_MNXM738068_e': 1000, 'EX_MNXM617_e': 1000, 'EX_MNXM1105810_e': 0, 'EX_MNXM37_e': 1000, 'EX_MNXM741173_e': 1000, 'EX_MNXM29_e': 1000, 'EX_MNXM490899_e': 1000, 'EX_MNXM733114_e': 1000, 'EX_MNXM60_e': 1000, 'EX_MNXM1107769_e': 1000, 'EX_MNXM728337_e': 1000, 'EX_MNXM1105941_e': 1000, 'EX_MNXM1104432_e': 0, 'EX_MNXM1106762_e': 1000, 'EX_MNXM729132_e': 1000, 'EX_MNXM1106164_e': 1000, 'EX_MNXM1106000_e': 0, 'EX_MNXM738804_e': 1000, 'EX_MNXM2397_e': 1000, 'EX_MNXM27_e': 1000, 'EX_MNXM274_e': 1000, 'EX_MNXM8_e': 1000, 'EX_MNXM729302_e': 1000, 'EX_MNXM732398_e': 1000, 'EX_MNXM741664_e': 1000, 'EX_MNXM249_e': 1000, 'EX_MNXM734864_e': 1000, 'EX_MNXM1094052_e': 1000, 'EX_MNXM114_e': 1000, 'EX_MNXM548_e': 1000, 'EX_MNXM419_e': 1000, 'EX_MNXM270_e': 1000, 'EX_MNXM737787_e': 1000, 'EX_MNXM1157_e': 1000, 'EX_MNXM730135_e': 1000, 'EX_MNXM142_e': 1000, 'EX_MNXM741553_e': 1000, 'EX_MNXM741004_e': 1000, 'EX_MNXM76_e': 1000, 'EX_MNXM158_e': 1000, 'EX_MNXM199_e': 1000, 'EX_MNXM174_e': 1000, 'EX_MNXM1108175_e': 0}\n",
      "No carbon source growth (control growth value):\n",
      "25.26944836056019\n",
      "Objective\n",
      "=========\n",
      "1.0 BIOMASS_Av_DJ_core = 25.26944836056019\n",
      "\n",
      "Uptake\n",
      "------\n",
      "   Metabolite         Reaction      Flux  C-Number C-Flux\n",
      "MNXM1106164_e EX_MNXM1106164_e      3.54         6  0.16%\n",
      "MNXM1107753_e EX_MNXM1107753_e     100.4         6  4.42%\n",
      "MNXM1107769_e EX_MNXM1107769_e      2.95         6  0.13%\n",
      "MNXM1107821_e EX_MNXM1107821_e     3.198         4  0.09%\n",
      "    MNXM128_e     EX_MNXM128_e    0.1315         0  0.00%\n",
      "    MNXM142_e     EX_MNXM142_e     11.04         4  0.32%\n",
      "    MNXM158_e     EX_MNXM158_e     8.359         4  0.25%\n",
      "      MNXM1_e       EX_MNXM1_e     50.62         0  0.00%\n",
      "   MNXM2255_e    EX_MNXM2255_e   0.01746         0  0.00%\n",
      "    MNXM274_e     EX_MNXM274_e   0.05756         6  0.00%\n",
      "    MNXM304_e     EX_MNXM304_e 5.054E-05        10  0.00%\n",
      "     MNXM37_e      EX_MNXM37_e     560.2         5 20.54%\n",
      " MNXM490899_e  EX_MNXM490899_e      1000        10 73.32%\n",
      "     MNXM58_e      EX_MNXM58_e    0.1096         0  0.00%\n",
      "    MNXM653_e     EX_MNXM653_e    0.2192         0  0.00%\n",
      " MNXM726092_e  EX_MNXM726092_e 0.0001769         0  0.00%\n",
      " MNXM726711_e  EX_MNXM726711_e    0.2085         0  0.00%\n",
      " MNXM726712_e  EX_MNXM726712_e    0.1973         0  0.00%\n",
      " MNXM729215_e  EX_MNXM729215_e  0.008617         0  0.00%\n",
      " MNXM731166_e  EX_MNXM731166_e   0.01792         0  0.00%\n",
      " MNXM731950_e  EX_MNXM731950_e  0.008162         0  0.00%\n",
      " MNXM732398_e  EX_MNXM732398_e     379.7         0  0.00%\n",
      " MNXM733114_e  EX_MNXM733114_e     6.146         5  0.23%\n",
      " MNXM734864_e  EX_MNXM734864_e   0.01703         9  0.00%\n",
      " MNXM735438_e  EX_MNXM735438_e      1000         0  0.00%\n",
      " MNXM735978_e  EX_MNXM735978_e    0.1315         0  0.00%\n",
      " MNXM737787_e  EX_MNXM737787_e     24.88         3  0.55%\n",
      "  MNXM90960_e   EX_MNXM90960_e 0.0006317         0  0.00%\n",
      "     MNXM95_e      EX_MNXM95_e     4.932         0  0.00%\n",
      "      MNXM9_e       EX_MNXM9_e     24.38         0  0.00%\n",
      "      WATER_e       EX_WATER_e     906.5         0  0.00%\n",
      "\n",
      "Secretion\n",
      "---------\n",
      "   Metabolite    Reaction      Flux  C-Number C-Flux\n",
      "    MNXM828_c DM_4crsol_c -0.005635         7  0.00%\n",
      " MNXM736134_c  DM_5drib_c -0.005635         5  0.00%\n",
      "    MNXM168_e    EX_ade_e -0.005635         5  0.00%\n",
      "MNXM1105731_e EX_ala__D_e   -0.3511         3  0.01%\n",
      "MNXM1108206_e EX_asp__L_e    -969.5         4 30.70%\n",
      "    MNXM683_e   EX_cgly_e      -996         5 39.43%\n",
      "     MNXM13_e    EX_co2_e     -1000         1  7.92%\n",
      "MNXM1105052_e EX_dxylnt_e  -0.01691         5  0.00%\n",
      "MNXM1108092_e   EX_etoh_e    -84.21         2  1.33%\n",
      "        nh4_e    EX_nh4_e     -1000         0  0.00%\n",
      "    MNXM107_e    EX_no2_e    -379.7         0  0.00%\n",
      "     MNXM25_e   EX_succ_e    -650.6         4 20.61%\n",
      "\n",
      "MNXM726888_e\n",
      "25.269448360560112\n",
      "MNXM1105810_e\n",
      "31.297825143881756\n",
      "MNXM1137670_e\n",
      "31.591408020625707\n",
      "MNXM1106000_e\n",
      "31.591408020625817\n",
      "MNXM1104432_e\n",
      "25.26944836056006\n",
      "MNXM1108175_e\n",
      "31.59140802062592\n",
      "No carbon source growth:\n",
      "21.586502611559705\n",
      "Objective\n",
      "=========\n",
      "1.0 BIOMASS_Av_DJ_core = 21.586502611559705\n",
      "\n",
      "Uptake\n",
      "------\n",
      "   Metabolite         Reaction      Flux  C-Number C-Flux\n",
      "MNXM1107753_e EX_MNXM1107753_e     295.6         6 14.99%\n",
      "    MNXM128_e     EX_MNXM128_e    0.1124         0  0.00%\n",
      "    MNXM158_e     EX_MNXM158_e     7.141         4  0.24%\n",
      "      MNXM1_e       EX_MNXM1_e     236.7         0  0.00%\n",
      "   MNXM2255_e    EX_MNXM2255_e   0.01492         0  0.00%\n",
      "    MNXM274_e     EX_MNXM274_e   0.04917         6  0.00%\n",
      "    MNXM304_e     EX_MNXM304_e 4.317E-05        10  0.00%\n",
      " MNXM490899_e  EX_MNXM490899_e      1000        10 84.54%\n",
      "     MNXM58_e      EX_MNXM58_e   0.09364         0  0.00%\n",
      "    MNXM653_e     EX_MNXM653_e    0.1873         0  0.00%\n",
      " MNXM726092_e  EX_MNXM726092_e 0.0001511         0  0.00%\n",
      " MNXM726711_e  EX_MNXM726711_e    0.1782         0  0.00%\n",
      " MNXM726712_e  EX_MNXM726712_e    0.1685         0  0.00%\n",
      " MNXM729215_e  EX_MNXM729215_e  0.007361         0  0.00%\n",
      " MNXM731166_e  EX_MNXM731166_e    0.0153         0  0.00%\n",
      " MNXM731950_e  EX_MNXM731950_e  0.006972         0  0.00%\n",
      " MNXM733114_e  EX_MNXM733114_e      5.25         5  0.22%\n",
      " MNXM734864_e  EX_MNXM734864_e   0.01455         9  0.00%\n",
      " MNXM735438_e  EX_MNXM735438_e     904.4         0  0.00%\n",
      " MNXM735978_e  EX_MNXM735978_e    0.1124         0  0.00%\n",
      "  MNXM90960_e   EX_MNXM90960_e 0.0005397         0  0.00%\n",
      "     MNXM95_e      EX_MNXM95_e     4.214         0  0.00%\n",
      "      MNXM9_e       EX_MNXM9_e     20.82         0  0.00%\n",
      "      WATER_e       EX_WATER_e     306.3         0  0.00%\n",
      "\n",
      "Secretion\n",
      "---------\n",
      "   Metabolite         Reaction      Flux  C-Number C-Flux\n",
      "    MNXM828_c      DM_4crsol_c -0.004814         7  0.00%\n",
      " MNXM736134_c       DM_5drib_c -0.004814         5  0.00%\n",
      "MNXM1108206_e EX_MNXM1108206_e    -577.9         4 21.08%\n",
      "    MNXM168_e     EX_MNXM168_e -0.004814         5  0.00%\n",
      "MNXM1105731_e      EX_ala__D_e   -0.2999         3  0.01%\n",
      "    MNXM683_e        EX_cgly_e    -996.6         5 45.44%\n",
      "     MNXM13_e         EX_co2_e     -1000         1  9.12%\n",
      "MNXM1105052_e      EX_dxylnt_e  -0.01444         5  0.00%\n",
      "        nh4_e         EX_nh4_e    -243.4         0  0.00%\n",
      "     MNXM25_e        EX_succ_e    -667.9         4 24.36%\n",
      "\n",
      "MNXM726888_e\n",
      "21.58650261155974\n",
      "MNXM738068_e\n",
      "21.58650261155994\n",
      "MNXM1105810_e\n",
      "27.363195845451312\n",
      "MNXM1137670_e\n",
      "27.63383624494601\n",
      "MNXM1107769_e\n",
      "21.83498635908588\n",
      "MNXM1106000_e\n",
      "27.633836244945986\n",
      "MNXM1105732_e\n",
      "21.586502611559855\n",
      "MNXM739527_e\n",
      "21.586502611559855\n",
      "MNXM1107821_e\n",
      "21.645846998529457\n",
      "MNXM1108206_e\n",
      "21.58650261155985\n",
      "MNXM37_e\n",
      "24.712080213769685\n",
      "MNXM741173_e\n",
      "21.586502611559894\n",
      "MNXM29_e\n",
      "21.586502611559894\n",
      "MNXM728337_e\n",
      "21.586502611559894\n",
      "MNXM1106762_e\n",
      "21.586502611559894\n",
      "MNXM1106164_e\n",
      "21.61930760376035\n",
      "MNXM738804_e\n",
      "21.58650261155976\n",
      "MNXM741664_e\n",
      "21.586502611559894\n",
      "MNXM114_e\n",
      "21.586502611559894\n",
      "MNXM737787_e\n",
      "21.657545535095654\n",
      "MNXM142_e\n",
      "21.68917123093798\n",
      "MNXM741553_e\n",
      "21.58650261155964\n",
      "MNXM76_e\n",
      "21.58650261155982\n",
      "MNXM199_e\n",
      "21.58650261155982\n",
      "MNXM1104432_e\n",
      "21.58650261155982\n",
      "MNXM1108175_e\n",
      "27.633836244945893\n"
     ]
    }
   ],
   "source": [
    "default_growth_rate_list = []\n",
    "\n",
    "output_major_carbon_sources = pd.DataFrame(major_carbon_sources, index=[0])\n",
    "output_major_carbon_sources = output_major_carbon_sources.transpose()\n",
    "\n",
    "output_minor_carbon_sources = pd.DataFrame(minor_carbon_sources, index=[0])\n",
    "output_minor_carbon_sources = output_minor_carbon_sources.transpose()\n",
    "\n",
    "no_c_growth_major_list = []\n",
    "no_c_growth_minor_list = []\n",
    "\n",
    "model_list = [modelID]\n",
    "\n",
    "for modelID in model_list:\n",
    "    \n",
    "    model_path = project_dir + modelID\n",
    "    print(model_path)\n",
    "    model = read_sbml_model(model_path)\n",
    "    ## Create no-carbon medium\n",
    "    print(modelID)\n",
    "    print(model_path)\n",
    "    no_c_medium = model.medium # use full model media as template to create no-C\n",
    "    print(no_c_medium)\n",
    "\n",
    "\n",
    "    specific_media = M8_media.copy()\n",
    "\n",
    "    # Set media-specific metabolites to 1000\n",
    "    for met in specific_media:\n",
    "        if met not in model.metabolites:\n",
    "            #print(\"adding metabolite:\")\n",
    "            #print(met)\n",
    "            model.add_metabolites([Metabolite(\n",
    "                    met,\n",
    "                    compartment ='e'),])\n",
    "        \n",
    "        if f\"EX_{met}\" not in model.reactions:  \n",
    "            print(met)\n",
    "            model.add_boundary(model.metabolites.get_by_id(met), type = \"exchange\")\n",
    "            model.repair() # mentioned here: https://cobrapy.readthedocs.io/en/latest/faq.html\n",
    "        no_c_medium[f\"EX_{met}\"] = 1000\n",
    "    \n",
    "    model.medium = no_c_medium\n",
    "    print(\"default growth rate:\")\n",
    "    default_growth = model.slim_optimize()\n",
    "    print(default_growth)\n",
    "    default_growth_rate_list.append(default_growth)\n",
    "    \n",
    "    ## LOOP THROUGH MAJOR CARBON SOURCES    \n",
    "    \n",
    "    # Ensure carbon sources are all zero (even if they were in media)\n",
    "    for met in major_carbon_sources:\n",
    "        if met not in model.metabolites:\n",
    "            #print(\"adding metabolite:\")\n",
    "            #print(met)\n",
    "            model.add_metabolites([Metabolite(\n",
    "                    met,\n",
    "                    compartment ='C_e'),])\n",
    "        \n",
    "        if f\"EX_{met}\" not in model.reactions: \n",
    "            model.add_boundary(model.metabolites.get_by_id(met), type = \"exchange\")\n",
    "            model.repair() # mentioned here: https://cobrapy.readthedocs.io/en/latest/faq.html\n",
    "        no_c_medium[f\"EX_{met}\"] = 0\n",
    "    \n",
    "    # Confirm that the model will not grow once all these are set to zero\n",
    "    \n",
    "    print(no_c_medium)\n",
    "    model.medium = no_c_medium\n",
    "    print(\"No carbon source growth (control growth value):\")\n",
    "    no_c_growth = model.slim_optimize()\n",
    "    no_c_growth_major_list.append(no_c_growth)\n",
    "        \n",
    "    print(no_c_growth) \n",
    "    print(model.summary())\n",
    "\n",
    "    ## Loop through C sources\n",
    "    # running the FBA with one C source at a time\n",
    "    c_source_list = []\n",
    "    for met in major_carbon_sources:\n",
    "        print(met)\n",
    "        with model:\n",
    "            medium = model.medium\n",
    "            medium[f\"EX_{met}\"] = 1000\n",
    "            model.medium = medium\n",
    "            growth = model.slim_optimize()\n",
    "            print(growth)\n",
    "            c_source_list.append(growth)\n",
    "    \n",
    "    output_major_carbon_sources[modelID] = c_source_list\n",
    "    \n",
    "    \n",
    "    \n",
    "    ## LOOP THROUGH MINOR CARBON SOURCES    \n",
    "    # Ensure carbon sources are all zero (even if they were in media)\n",
    "    for met in minor_carbon_sources:\n",
    "        if met not in model.metabolites:\n",
    "            #print(\"adding metabolite:\")\n",
    "            #print(met)\n",
    "            model.add_metabolites([Metabolite(\n",
    "                    met,\n",
    "                    compartment ='C_e'),])\n",
    "        \n",
    "        if f\"EX_{met}\" not in model.reactions:  \n",
    "            #model.add_boundary(met)\n",
    "            model.add_boundary(model.metabolites.get_by_id(met), type = \"exchange\")\n",
    "            model.repair() # mentioned here: https://cobrapy.readthedocs.io/en/latest/faq.html\n",
    "        no_c_medium[f\"EX_{met}\"] = 0\n",
    "    \n",
    "    # Confirm that the model will not grow once all these are set to zero\n",
    "    #print(no_c_medium)\n",
    "    model.medium = no_c_medium\n",
    "    \n",
    "    print(\"No carbon source growth:\")\n",
    "    no_c_growth = model.slim_optimize()\n",
    "    no_c_growth_minor_list.append(no_c_growth)\n",
    "    \n",
    "    c_source_list = []\n",
    "    #c_source_list.append(no_c_growth)\n",
    "    \n",
    "    print(no_c_growth) \n",
    "    print(model.summary())\n",
    "    \n",
    "    \n",
    "    ## Loop through C sources\n",
    "    # running the FBA with one C source at a time\n",
    "    for met in minor_carbon_sources:\n",
    "        print(met)\n",
    "        with model:\n",
    "            medium = model.medium\n",
    "            medium[f\"EX_{met}\"] = 1000\n",
    "            model.medium = medium\n",
    "            growth = model.slim_optimize()\n",
    "            print(growth)\n",
    "            c_source_list.append(growth)\n",
    "    output_minor_carbon_sources[modelID] = c_source_list  \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "255791e4-6632-4719-a318-c6d4159454a7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Objective\n",
      "=========\n",
      "1.0 BIOMASS_Av_DJ_core = 25.26944836056019\n",
      "\n",
      "Uptake\n",
      "------\n",
      "   Metabolite         Reaction      Flux  C-Number C-Flux\n",
      "MNXM1106164_e EX_MNXM1106164_e      3.54         6  0.16%\n",
      "MNXM1107753_e EX_MNXM1107753_e     100.4         6  4.42%\n",
      "MNXM1107769_e EX_MNXM1107769_e      2.95         6  0.13%\n",
      "MNXM1107821_e EX_MNXM1107821_e     3.198         4  0.09%\n",
      "    MNXM128_e     EX_MNXM128_e    0.1315         0  0.00%\n",
      "    MNXM142_e     EX_MNXM142_e     11.04         4  0.32%\n",
      "    MNXM158_e     EX_MNXM158_e     8.359         4  0.25%\n",
      "      MNXM1_e       EX_MNXM1_e     50.62         0  0.00%\n",
      "   MNXM2255_e    EX_MNXM2255_e   0.01746         0  0.00%\n",
      "    MNXM274_e     EX_MNXM274_e   0.05756         6  0.00%\n",
      "    MNXM304_e     EX_MNXM304_e 5.054E-05        10  0.00%\n",
      "     MNXM37_e      EX_MNXM37_e     560.2         5 20.54%\n",
      " MNXM490899_e  EX_MNXM490899_e      1000        10 73.32%\n",
      "     MNXM58_e      EX_MNXM58_e    0.1096         0  0.00%\n",
      "    MNXM653_e     EX_MNXM653_e    0.2192         0  0.00%\n",
      " MNXM726092_e  EX_MNXM726092_e 0.0001769         0  0.00%\n",
      " MNXM726711_e  EX_MNXM726711_e    0.2085         0  0.00%\n",
      " MNXM726712_e  EX_MNXM726712_e    0.1973         0  0.00%\n",
      " MNXM729215_e  EX_MNXM729215_e  0.008617         0  0.00%\n",
      " MNXM731166_e  EX_MNXM731166_e   0.01792         0  0.00%\n",
      " MNXM731950_e  EX_MNXM731950_e  0.008162         0  0.00%\n",
      " MNXM732398_e  EX_MNXM732398_e     379.7         0  0.00%\n",
      " MNXM733114_e  EX_MNXM733114_e     6.146         5  0.23%\n",
      " MNXM734864_e  EX_MNXM734864_e   0.01703         9  0.00%\n",
      " MNXM735438_e  EX_MNXM735438_e      1000         0  0.00%\n",
      " MNXM735978_e  EX_MNXM735978_e    0.1315         0  0.00%\n",
      " MNXM737787_e  EX_MNXM737787_e     24.88         3  0.55%\n",
      "  MNXM90960_e   EX_MNXM90960_e 0.0006317         0  0.00%\n",
      "     MNXM95_e      EX_MNXM95_e     4.932         0  0.00%\n",
      "      MNXM9_e       EX_MNXM9_e     24.38         0  0.00%\n",
      "      WATER_e       EX_WATER_e     906.5         0  0.00%\n",
      "\n",
      "Secretion\n",
      "---------\n",
      "   Metabolite    Reaction      Flux  C-Number C-Flux\n",
      "    MNXM828_c DM_4crsol_c -0.005635         7  0.00%\n",
      " MNXM736134_c  DM_5drib_c -0.005635         5  0.00%\n",
      "    MNXM168_e    EX_ade_e -0.005635         5  0.00%\n",
      "MNXM1105731_e EX_ala__D_e   -0.3511         3  0.01%\n",
      "MNXM1108206_e EX_asp__L_e    -969.5         4 30.70%\n",
      "    MNXM683_e   EX_cgly_e      -996         5 39.43%\n",
      "     MNXM13_e    EX_co2_e     -1000         1  7.92%\n",
      "MNXM1105052_e EX_dxylnt_e  -0.01691         5  0.00%\n",
      "MNXM1108092_e   EX_etoh_e    -84.21         2  1.33%\n",
      "        nh4_e    EX_nh4_e     -1000         0  0.00%\n",
      "    MNXM107_e    EX_no2_e    -379.7         0  0.00%\n",
      "     MNXM25_e   EX_succ_e    -650.6         4 20.61%\n",
      "\n"
     ]
    }
   ],
   "source": [
    "    print(model.summary())\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "5784ad09-cfb4-4ef2-8432-68a680df2b1d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 iAA1300/iAA1300_modified_cobra.xml\n",
      "0                          31.591408\n"
     ]
    }
   ],
   "source": [
    "default_growth_rate = pd.DataFrame(default_growth_rate_list)\n",
    "model = pd.DataFrame(model_list)\n",
    "\n",
    "default_growth_rate_df = pd.concat([model, default_growth_rate], axis = 1)\n",
    "default_growth_rate_df = default_growth_rate_df.transpose()\n",
    "default_growth_rate_df.columns = default_growth_rate_df.iloc[0]\n",
    "output_default_growth_rate = default_growth_rate_df.iloc[pd.RangeIndex(len(default_growth_rate_df)).drop(0)]\n",
    "print(output_default_growth_rate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "f9adb858-4a8f-4567-a6ca-e065ac1fd607",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "               0  iAA1300/iAA1300_modified_cobra.xml\n",
      "MNXM726888_e   0                           25.269448\n",
      "MNXM1105810_e  0                           31.297825\n",
      "MNXM1137670_e  0                           31.591408\n",
      "MNXM1106000_e  0                           31.591408\n",
      "MNXM1104432_e  0                           25.269448\n",
      "MNXM1108175_e  0                           31.591408\n"
     ]
    }
   ],
   "source": [
    "print(output_major_carbon_sources)\n",
    "#print(output_minor_carbon_sources)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "2818c65f-47d8-48e7-82b0-82eadb6c4efc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 iAA1300/iAA1300_modified_cobra.xml\n",
      "0                          25.269448\n"
     ]
    }
   ],
   "source": [
    "no_c_growth_major = pd.DataFrame(no_c_growth_major_list)\n",
    "model = pd.DataFrame(model_list)\n",
    "\n",
    "no_c_growth_major_df = pd.concat([model, no_c_growth_major], axis = 1)\n",
    "no_c_growth_major_df = no_c_growth_major_df.transpose()\n",
    "no_c_growth_major_df.columns = no_c_growth_major_df.iloc[0]\n",
    "output_no_c_growth_major = no_c_growth_major_df.iloc[pd.RangeIndex(len(no_c_growth_major_df)).drop(0)]\n",
    "print(output_no_c_growth_major)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "7b1ea158-3e57-48ec-8c24-ef0db91296ec",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 iAA1300/iAA1300_modified_cobra.xml\n",
      "0                          21.586503\n"
     ]
    }
   ],
   "source": [
    "no_c_growth_minor = pd.DataFrame(no_c_growth_minor_list)\n",
    "model = pd.DataFrame(model_list)\n",
    "\n",
    "no_c_growth_minor_df = pd.concat([model, no_c_growth_minor], axis = 1)\n",
    "no_c_growth_minor_df = no_c_growth_minor_df.transpose()\n",
    "no_c_growth_minor_df.columns = no_c_growth_minor_df.iloc[0]\n",
    "output_no_c_growth_minor = no_c_growth_minor_df.iloc[pd.RangeIndex(len(no_c_growth_minor_df)).drop(0)]\n",
    "print(output_no_c_growth_minor)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "6ebe92cb-d9a2-4378-88fd-feb63843ae09",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "              iAA1300/iAA1300_modified_cobra.xml    0\n",
      "0                                      25.269448  NaN\n",
      "MNXM726888_e                           25.269448  0.0\n",
      "MNXM1105810_e                          31.297825  0.0\n",
      "MNXM1137670_e                          31.591408  0.0\n",
      "MNXM1106000_e                          31.591408  0.0\n",
      "MNXM1104432_e                          25.269448  0.0\n",
      "MNXM1108175_e                          31.591408  0.0\n",
      "              iAA1300/iAA1300_modified_cobra.xml    0\n",
      "0                                      21.586503  NaN\n",
      "MNXM726888_e                           21.586503  0.0\n",
      "MNXM738068_e                           21.586503  0.0\n",
      "MNXM1105810_e                          27.363196  0.0\n",
      "MNXM1137670_e                          27.633836  0.0\n",
      "MNXM1107769_e                          21.834986  0.0\n",
      "MNXM1106000_e                          27.633836  0.0\n",
      "MNXM1105732_e                          21.586503  0.0\n",
      "MNXM739527_e                           21.586503  0.0\n",
      "MNXM1107821_e                          21.645847  0.0\n",
      "MNXM1108206_e                          21.586503  0.0\n",
      "MNXM37_e                                24.71208  0.0\n",
      "MNXM741173_e                           21.586503  0.0\n",
      "MNXM29_e                               21.586503  0.0\n",
      "MNXM728337_e                           21.586503  0.0\n",
      "MNXM1106762_e                          21.586503  0.0\n",
      "MNXM1106164_e                          21.619308  0.0\n",
      "MNXM738804_e                           21.586503  0.0\n",
      "MNXM741664_e                           21.586503  0.0\n",
      "MNXM114_e                              21.586503  0.0\n",
      "MNXM737787_e                           21.657546  0.0\n",
      "MNXM142_e                              21.689171  0.0\n",
      "MNXM741553_e                           21.586503  0.0\n",
      "MNXM76_e                               21.586503  0.0\n",
      "MNXM199_e                              21.586503  0.0\n",
      "MNXM1104432_e                          21.586503  0.0\n",
      "MNXM1108175_e                          27.633836  0.0\n"
     ]
    }
   ],
   "source": [
    "output_major_carbon_sources = pd.concat([output_no_c_growth_major, output_major_carbon_sources], axis = 0)\n",
    "output_minor_carbon_sources = pd.concat([output_no_c_growth_minor, output_minor_carbon_sources], axis = 0)\n",
    "\n",
    "print(output_major_carbon_sources)\n",
    "print(output_minor_carbon_sources)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c1511ba2-94c9-436b-985c-9a72abefbabc",
   "metadata": {},
   "outputs": [],
   "source": [
    "# reading out C source loop output as a csv file for Gram negative M8 (complete) media gap-filled models\n",
    "output_major_carbon_sources.to_csv(path_or_buf = project_dir + \"output_major_carbon_sources_M8.csv\", \n",
    "                                   sep = \",\")\n",
    "output_minor_carbon_sources.to_csv(path_or_buf = project_dir + \"output_minor_carbon_sources_M8.csv\", \n",
    "                                   sep = \",\")"
   ]
  },
  {
   "cell_type": "raw",
   "id": "2e0ed129-6e76-4266-bd59-de2bacdf42c4",
   "metadata": {},
   "source": [
    "import memote"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "cd86034d-6678-49ee-8da5-be962e06f4e1",
   "metadata": {},
   "outputs": [
    {
     "ename": "ModuleNotFoundError",
     "evalue": "No module named 'memote'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[31], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmemote\u001b[39;00m\n",
      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'memote'"
     ]
    }
   ],
   "source": [
    "import memote"
   ]
  }
 ],
 "metadata": {
  "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": "3.12.2"
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 },
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