Adding carbon source analysis

Author: cshenry

CarbonSources/BiologFeatureAnalysis.ipynb

@@ -0,0 +1,121 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "python version 3.7.6\n",
+      "cobrakbase 0.2.8\n",
+      "Required modules loaded\n"
+     ]
+    }
+   ],
+   "source": [
+    "import platform\n",
+    "print(\"python version \" + platform.python_version())\n",
+    "import sys\n",
+    "import json\n",
+    "import cobra\n",
+    "import cplex\n",
+    "import re\n",
+    "import os\n",
+    "from os.path import exists\n",
+    "import logging\n",
+    "from configparser import ConfigParser\n",
+    "config = ConfigParser()\n",
+    "config.read(\"config.cfg\")\n",
+    "paths = config.get(\"script\", \"syspaths\").split(\";\")\n",
+    "for path in paths:\n",
+    "    sys.path.append(path)\n",
+    "import cobrakbase\n",
+    "import cobra\n",
+    "from escher import Builder\n",
+    "from optlang.symbolics import Zero, add\n",
+    "from modelseedpy import MSPackageManager, MSGapfill, FBAHelper, MSGrowthPhenotypes, MSModelUtil, MSATPCorrection\n",
+    "from cobrakbase.core.kbasefba.newmodeltemplate_builder import NewModelTemplateBuilder\n",
+    "from annotation_ontology_api.annotation_ontology_apiServiceClient import annotation_ontology_api\n",
+    "from modelseedpy.helpers import get_template\n",
+    "from sklearn.metrics import r2_score\n",
+    "%matplotlib inline\n",
+    "import matplotlib.pyplot as plt\n",
+    "import pandas as pd\n",
+    "from IPython.display import HTML\n",
+    "print(\"Required modules loaded\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#First we pull all the Biolog datasets out of Kbase\n",
+    "#kbase_api = cobrakbase.KBaseAPI()\n",
+    "biologs = kbase_api.list_objects(101536, object_type=\"KBasePhenotypes.PhenotypeSet\", include_metadata=True)\n",
+    "genome_biologs = {}\n",
+    "for item in biologs:\n",
+    "    if \"GenomeID\" in item[10]:\n",
+    "        kbpheno = kbase_api.get_object(item[1], 101536)\n",
+    "        genome_biologs[item[10][\"GenomeID\"]] = MSGrowthPhenotypes.from_kbase_object(kbpheno,kbase_api)\n",
+    "#Now we iterate over the biolog datasets, pull the model, and simulate the phenotypes\n",
+    "template = kbase_api.get_from_ws(\"GramNegModelTemplateV3\",\"NewKBaseModelTemplates\")\n",
+    "pheno_frequency = {}\n",
+    "pheno_reactions = {}\n",
+    "for genome in genome_biologs:\n",
+    "    if exists(\"GFModels/RAST/\"+genome+\".json\"):\n",
+    "        model = cobra.io.load_json_model(\"GFModels/RAST/\"+genome+\".json\")\n",
+    "        for pheno in genome_biologs[genome].phenotypes:\n",
+    "            if pheno.id not in pheno_frequency:\n",
+    "                pheno_frequency[pheno.id] = 0\n",
+    "                pheno_reactions[pheno.id] = {}\n",
+    "            pheno_frequency[pheno.id] += 1\n",
+    "            if pheno.growth > 0:\n",
+    "                output = pheno.simulate(model,add_missing_exchanges=True,save_fluxes=True,pfba=True)\n",
+    "                if output[\"growth\"] < 0.00001:\n",
+    "                    pheno.gapfill_model_for_phenotype(model,[template],None,add_missing_exchanges=True)\n",
+    "                    output = pheno.simulate(model,add_missing_exchanges=True,save_fluxes=True,pfba=True)\n",
+    "                if output[\"growth\"] > 0.01:\n",
+    "                    for rxn, value in output[\"fluxes\"].items():\n",
+    "                        if abs(value) > 0:\n",
+    "                            if rxn not in pheno_reactions[pheno.id]:\n",
+    "                                pheno_reactions[pheno.id][rxn] = 0\n",
+    "                            pheno_reactions[pheno.id][rxn] += 1\n",
+    "        df = pd.DataFrame(pheno_reactions)\n",
+    "        df.to_csv(\"BiologFeatureAnalysis.csv\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}