bx-python-intervaltree-issue.ipynb

{
 "metadata": {
  "name": "",
  "signature": "sha256:e7a95ff96eced6e3e0f91b11410c2548433f07afeb21c4bd5ca668d482dba258"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from bx.intervals.intersection import Interval, IntervalTree"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree = IntervalTree()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree.insert(5, 7, 'foo')\n",
      "tree.insert(9, 12, 'bar')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree.find(6, 8)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 5,
       "text": [
        "['foo']"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree.before(14)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "AttributeError",
       "evalue": "'str' object has no attribute 'end'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-11-3370fddbaf8e>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mtree\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mbefore\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m14\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalTree.before (lib/bx/intervals/intersection.c:4529)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalNode.left (lib/bx/intervals/intersection.c:2732)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;31mAttributeError\u001b[0m: 'str' object has no attribute 'end'"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree.before_interval(Interval(14, 16))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "AttributeError",
       "evalue": "'str' object has no attribute 'end'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-12-ddc5a057c3db>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mtree\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mbefore_interval\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mInterval\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m14\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m16\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalTree.before_interval (lib/bx/intervals/intersection.c:4877)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalNode.left (lib/bx/intervals/intersection.c:2732)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;31mAttributeError\u001b[0m: 'str' object has no attribute 'end'"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree.after(4)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "AttributeError",
       "evalue": "'str' object has no attribute 'start'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-7-896a39c1ddb7>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mtree\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mafter\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalTree.after (lib/bx/intervals/intersection.c:4668)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalNode.right (lib/bx/intervals/intersection.c:3020)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;31mAttributeError\u001b[0m: 'str' object has no attribute 'start'"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "tree.after_interval(Interval(2, 4))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "AttributeError",
       "evalue": "'str' object has no attribute 'start'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-10-abd657fa9fc5>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mtree\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mafter_interval\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mInterval\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m4\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalTree.after_interval (lib/bx/intervals/intersection.c:5021)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;32m/home/aliman/pyenv/scientific/local/lib/python2.7/site-packages/bx/intervals/intersection.so\u001b[0m in \u001b[0;36mbx.intervals.intersection.IntervalNode.right (lib/bx/intervals/intersection.c:3020)\u001b[1;34m()\u001b[0m\n",
        "\u001b[1;31mAttributeError\u001b[0m: 'str' object has no attribute 'start'"
       ]
      }
     ],
     "prompt_number": 10
    }
   ],
   "metadata": {}
  }
 ]
}