{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import logging"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "logging.basicConfig(level=\"DEBUG\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "DEBUG:optlang.util:Gurobi python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/gurobipy\n",
      "DEBUG:optlang.util:GLPK python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/swiglpk\n",
      "DEBUG:optlang.util:Mosek python bindings not available.\n",
      "DEBUG:optlang.util:CPLEX python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/cplex\n",
      "DEBUG:optlang.util:Scipy solver not available\n",
      "DEBUG:pip._internal.utils.misc:lzma module is not available\n",
      "DEBUG:pip._internal.vcs:Registered VCS backend: git\n",
      "DEBUG:pip._internal.vcs:Registered VCS backend: hg\n",
      "DEBUG:pip._internal.vcs:Registered VCS backend: svn\n",
      "DEBUG:pip._internal.vcs:Registered VCS backend: bzr\n"
     ]
    }
   ],
   "source": [
    "from cobra.test import create_test_model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.flux_analysis import single_gene_deletion"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "model = create_test_model(\"textbook\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "genes = ['b0008', 'b0114', 'b2276', 'b1779']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver = \"cplex\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "logging.getLogger().setLevel(logging.DEBUG)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 308 ms, sys: 0 ns, total: 308 ms\n",
      "Wall time: 307 ms\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>growth</th>\n",
       "      <th>status</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ids</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(b1779)</th>\n",
       "      <td>5.034815e+00</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b2276)</th>\n",
       "      <td>5.475871e+00</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b0114)</th>\n",
       "      <td>1.224159e+00</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b0008)</th>\n",
       "      <td>3.028591e-15</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      ],
      "text/plain": [
       "               growth   status\n",
       "ids                           \n",
       "(b1779)  5.034815e+00  optimal\n",
       "(b2276)  5.475871e+00  optimal\n",
       "(b0114)  1.224159e+00  optimal\n",
       "(b0008)  3.028591e-15  optimal"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time single_gene_deletion(model, method=\"linear room\", gene_list=genes, processes=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver = \"gurobi\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 271 ms, sys: 0 ns, total: 271 ms\n",
      "Wall time: 265 ms\n"
     ]
    },
    {
     "data": {
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       "      <th>(b1779)</th>\n",
       "      <td>5.034815</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b2276)</th>\n",
       "      <td>5.475871</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b0114)</th>\n",
       "      <td>1.224159</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b0008)</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>optimal</td>\n",
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       "  </tbody>\n",
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      "text/plain": [
       "           growth   status\n",
       "ids                       \n",
       "(b1779)  5.034815  optimal\n",
       "(b2276)  5.475871  optimal\n",
       "(b0114)  1.224159  optimal\n",
       "(b0008)  0.000000  optimal"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time single_gene_deletion(model, method=\"linear room\", gene_list=genes, processes=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver = \"glpk\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver.configuration.timeout = 20"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "DEBUG:optlang.glpk_interface:Status undefined. GLPK status code returned by glp_simplex was 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 205 ms, sys: 4.99 ms, total: 210 ms\n",
      "Wall time: 203 ms\n"
     ]
    },
    {
     "data": {
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(b1779)</th>\n",
       "      <td>5.034815e+00</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b2276)</th>\n",
       "      <td>5.475871e+00</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b0114)</th>\n",
       "      <td>1.224159e+00</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(b0008)</th>\n",
       "      <td>-5.857507e-17</td>\n",
       "      <td>optimal</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "               growth   status\n",
       "ids                           \n",
       "(b1779)  5.034815e+00  optimal\n",
       "(b2276)  5.475871e+00  optimal\n",
       "(b0114)  1.224159e+00  optimal\n",
       "(b0008) -5.857507e-17  optimal"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time single_gene_deletion(model, method=\"linear room\", gene_list=genes, processes=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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