IPython notebooks corresponding to Reagan et al, ISME Journal 2012

cloud_demo_complete.ipynb

cloud_demo_fast.ipynb

pearson_v_rf.ipynb

timing.ipynb

v3_v4_regions_only.ipynb

{
 "metadata": {
  "name": "v3 and v4 regions only"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!wget http://qiime.org/home_static/nih-cloud-apr2012/tree_metadata.txt\n!filter_distance_matrix.py -i /home/ubuntu/data/distance_matrix_complete.txt -o /home/ubuntu/data/distance_matrix_complete_v3_v4_only.txt -m tree_metadata.txt -s \"starting_v_region:v3,v4,full.length\"",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "--2012-08-07 20:05:42--  http://qiime.org/home_static/nih-cloud-apr2012/tree_metadata.txt\r\nResolving qiime.org... 216.34.181.97\r\nConnecting to qiime.org|216.34.181.97|:80... connected.\r\nHTTP request sent, awaiting response... "
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "200 OK\r\nLength: 9313 (9.1K) [text/plain]\r\nSaving to: `tree_metadata.txt.1'\r\n\r\n\r 0% [                                       ] 0           --.-K/s              \r100%[======================================>] 9,313       --.-K/s   in 0.02s   \r\n\r\n2012-08-07 20:05:42 (389 KB/s) - `tree_metadata.txt.1' saved [9313/9313]\r\n\r\n"
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!principal_coordinates.py -i /home/ubuntu/data/distance_matrix_complete_v3_v4_only.txt -o /home/ubuntu/data/pc_complete_v3_v4_only.txt",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!make_3d_plots.py -i /home/ubuntu/data/pc_complete_v3_v4_only.txt -o /home/ubuntu/data/pcoa_plots_complete_v3_v4_only/ -m tree_metadata.txt",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "And the notebook simply serves these files up in `/files`, so we can visit the visualization <a href=\"/files/data/pcoa_plots_complete_v3_v4_only/pc_complete_v3_v4_only_3D_PCoA_plots.html\" target=_blank>directly</a>\n\n**NOTE**: The above link is not static: to view the plot, you must run the notebook. "
    }
   ],
   "metadata": {}
  }
 ]
}

variable_region_position_calculations.ipynb