added data analysis for pagerank

rank/analyze_pagerank.ipynb

@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import json\n",
+    "import pickle\n",
+    "\n",
+    "uri2rank_filename = 'uri2rank_dump'\n",
+    "\n",
+    "def deserialize(filename):\n",
+    "    f = open(filename, 'rb')\n",
+    "    data = pickle.load(f)\n",
+    "    f.close()\n",
+    "    return data\n",
+    "\n",
+    "\n",
+    "def plot_histogram(ranks):\n",
+    "    plt.hist(ranks, bins=10000)\n",
+    "    plt.title('Pagerank distribution of iGEM parts')\n",
+    "    plt.xlabel('Pagerank value')\n",
+    "    plt.ylabel('Number of parts')\n",
+    "    plt.yscale('log', nonposy='clip')\n",
+    "    plt.xscale('log')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "('https://synbiohub.org/public/igem/igem2sbol/1', 0.6966999630711525)\n",
+      "[('https://synbiohub.org/public/igem/BBa_R0011/1', 0.0002486734703313158), ('https://synbiohub.org/public/igem/BBa_R0010/1', 0.0003709392326612267), ('https://synbiohub.org/public/igem/BBa_B0032/1', 0.00037285272469194823), ('https://synbiohub.org/public/igem/BBa_B0030/1', 0.0003802979168272833), ('https://synbiohub.org/public/igem/BBa_E0040/1', 0.0004580074863066108), ('https://synbiohub.org/public/igem/BBa_R0040/1', 0.00047659394938978373), ('https://synbiohub.org/public/igem/BBa_B0015/1', 0.000749152511989998), ('https://synbiohub.org/public/igem/BBa_B0010/1', 0.0014321551049507279), ('https://synbiohub.org/public/igem/BBa_B0012/1', 0.0014841141155577525), ('https://synbiohub.org/public/igem/BBa_B0034/1', 0.002044482861720468)]\n"
+     ]
+    }
+   ],
+   "source": [
+    "ranks = deserialize(uri2rank_filename)\n",
+    "ranks = list(filter(lambda item: 'sequence' not in item[0], ranks.items()))\n",
+    "ranks = sorted(ranks, key=lambda kv: kv[1])\n",
+    "\n",
+    "print(ranks[-1])\n",
+    "\n",
+    "print(ranks[-11:-1])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "image/png": 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\n",
+      "text/plain": [
+       "<Figure size 432x288 with 1 Axes>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "plot_histogram(list((map(lambda item: item[1], ranks[0:-1]))))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
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+}