From be7949c1c44231fbf7c737fe944eca2a57b37cf1 Mon Sep 17 00:00:00 2001
From: Luiz Irber <luiz.irber@gmail.com>
Date: Thu, 9 Aug 2018 20:16:15 +0000
Subject: [PATCH] debug notebooks

---
 notebooks/debug_graphs.ipynb         | 102 ++++++
 notebooks/nodegraph_similarity.ipynb | 445 +++++++++++++++++++++++++++
 2 files changed, 547 insertions(+)
 create mode 100644 notebooks/debug_graphs.ipynb
 create mode 100644 notebooks/nodegraph_similarity.ipynb

diff --git a/notebooks/debug_graphs.ipynb b/notebooks/debug_graphs.ipynb
new file mode 100644
index 0000000000..9b2168c580
--- /dev/null
+++ b/notebooks/debug_graphs.ipynb
@@ -0,0 +1,102 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from khmer import Nodegraph, Countgraph"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ng = Nodegraph(3, 10, 1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[0, 171, 134, 226, 57, 127, 0]"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ng.get_raw_tables()[0].tolist()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cg = Countgraph(3, 10, 1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[0, 0, 0, 0, 0, 0, 0]"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cg.get_raw_tables()[0].tolist()"
+   ]
+  }
+ ],
+ "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": "3.6.5"
+  },
+  "nav_menu": {},
+  "toc": {
+   "navigate_menu": true,
+   "number_sections": true,
+   "sideBar": true,
+   "threshold": 6,
+   "toc_cell": false,
+   "toc_section_display": "block",
+   "toc_window_display": false
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/notebooks/nodegraph_similarity.ipynb b/notebooks/nodegraph_similarity.ipynb
new file mode 100644
index 0000000000..d566318206
--- /dev/null
+++ b/notebooks/nodegraph_similarity.ipynb
@@ -0,0 +1,445 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 38,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from khmer import Nodegraph"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 50,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[0, 139, 170, 240, 110, 127, 0]"
+      ]
+     },
+     "execution_count": 50,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ng = Nodegraph(3, 10, 1)\n",
+    "ng.get_raw_tables()[0].tolist()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 51,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[1, 139, 170, 240, 110, 127, 0]"
+      ]
+     },
+     "execution_count": 51,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ng.count('AAA')\n",
+    "ng.get_raw_tables()[0].tolist()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[17, 139, 170, 240, 110, 127, 0]"
+      ]
+     },
+     "execution_count": 40,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ng.count('CGC')\n",
+    "ng.get_raw_tables()[0].tolist()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.5"
+      ]
+     },
+     "execution_count": 41,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "other_ng = Nodegraph(3, 10, 1)\n",
+    "other_ng.count('AAA')\n",
+    "ng.similarity(other_ng)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[1, 139, 170, 240, 110, 127, 0]"
+      ]
+     },
+     "execution_count": 42,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "other_ng.get_raw_tables()[0].tolist()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[17, 139, 170, 240, 110, 127, 0]"
+      ]
+     },
+     "execution_count": 43,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ng.get_raw_tables()[0].tolist()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 48,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def py_similarity(a, b):\n",
+    "    a_tables = a.get_raw_tables()\n",
+    "    b_tables = b.get_raw_tables()\n",
+    "    \n",
+    "    intersection = 0\n",
+    "    union_size = 0\n",
+    "    for i, (me, other) in enumerate(zip(a_tables, b_tables)):\n",
+    "        for v, t in zip(me.tolist(), other.tolist()):\n",
+    "            intersection += bin(v & t).count('1')\n",
+    "            union_size += bin(v | t).count('1')\n",
+    "            print(v, t, intersection, union_size)\n",
+    "    if union_size == 0:\n",
+    "        union_size = 1\n",
+    "    \n",
+    "    return intersection / union_size"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 49,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "17 1 1 2\n",
+      "139 139 5 6\n",
+      "170 170 9 10\n",
+      "240 240 13 14\n",
+      "110 110 18 19\n",
+      "127 127 25 26\n",
+      "0 0 25 26\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "0.9615384615384616"
+      ]
+     },
+     "execution_count": 49,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "py_similarity(ng, other_ng)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def similarity(a, b):\n",
+    "    return bin(a & b).count('1') / (bin(a | b).count('1') or 1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 18,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "similarity(0b0101,\n",
+    "           0b1010)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "similarity(0b0000,\n",
+    "           0b0000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "similarity(0b0000,\n",
+    "           0b0000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1.0"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "similarity(0b1111,\n",
+    "           0b1111)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.5"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "similarity(0b1010,\n",
+    "           0b1111)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def containment(a, b):\n",
+    "    return bin(a & b).count('1') / (bin(a).count('1') or 1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "containment(0b0101,\n",
+    "            0b1010)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "containment(0b0000,\n",
+    "            0b0000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "containment(0b0000,\n",
+    "            0b0000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1.0"
+      ]
+     },
+     "execution_count": 27,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "containment(0b1111,\n",
+    "            0b1111)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1.0"
+      ]
+     },
+     "execution_count": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "containment(0b1010,\n",
+    "            0b1111)"
+   ]
+  }
+ ],
+ "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": "3.6.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}