artifact-demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from feature_table.artifact_types.feature_table import FeatureTable, Frequency"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# this is temporarily in place for testing purposes\n",
    "import biom\n",
    "biom_path = \"/Users/caporaso/code/q2d2/example-data/keyboard/q191/otu-table.tsv\"\n",
    "#table = biom.util.biom_open(open(biom_path))\n",
    "table = biom.load_table(biom_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# Constructed from biom file\n",
      "#OTU ID\tK3.H\tK3.Z\tM2.Middle.L\tK3.A\tK3.R\n",
      "New.CleanUp.ReferenceOTU0\t2.0\t0.0\t0.0\t0.0\t0.0\n",
      "New.CleanUp.ReferenceOTU1\t0.0\t1.0\t6.0\t1.0\t1.0\n",
      "New.CleanUp.ReferenceOTU3\t0.0\t0.0\t0.0\t0.0\t0.0\n",
      "New.CleanUp.ReferenceOTU6\t0.0\t0.0\t0.0\t0.0\t0.0\n",
      "New.CleanUp.ReferenceOTU7\t0.0\t0.0\t0.0\t0.0\t0.0\n"
     ]
    }
   ],
   "source": [
    "print(table.head(n=5))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from qiime.sdk.artifact import Artifact"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "Artifact.save(table, FeatureTable[Frequency], \"nothing...\", \"./table.qtf\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/caporaso/Dropbox/code/feature-table/feature_table/workflows\r\n"
     ]
    }
   ],
   "source": [
    "!pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "a = Artifact('./table.qtf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<qiime.sdk.artifact.Artifact at 0x10dd22438>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "658 x 104 <class 'biom.table.Table'> with 5670 nonzero entries (8% dense)"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "UUID('6235ce1c-70e8-4559-b6a8-cdcbb6533d33')"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.uuid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'nothing...'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.provenance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# Constructed from biom file\n",
      "#OTU ID\tK3.H\tK3.Z\tM2.Middle.L\tK3.A\tK3.R\n",
      "New.CleanUp.ReferenceOTU0\t2.0\t0.0\t0.0\t0.0\t0.0\n",
      "New.CleanUp.ReferenceOTU1\t0.0\t1.0\t6.0\t1.0\t1.0\n",
      "New.CleanUp.ReferenceOTU3\t0.0\t0.0\t0.0\t0.0\t0.0\n",
      "New.CleanUp.ReferenceOTU6\t0.0\t0.0\t0.0\t0.0\t0.0\n",
      "New.CleanUp.ReferenceOTU7\t0.0\t0.0\t0.0\t0.0\t0.0\n"
     ]
    }
   ],
   "source": [
    "print(a.data.head(n=5))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "FeatureTable[Frequency]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.type"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "New.CleanUp.ReferenceOTU0    None\n",
       "New.CleanUp.ReferenceOTU1    None\n",
       "New.CleanUp.ReferenceOTU3    None\n",
       "New.CleanUp.ReferenceOTU6    None\n",
       "New.CleanUp.ReferenceOTU7    None\n",
       "dtype: object"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.type.get_columns(a.data)[:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "K3.H           2\n",
       "K3.Z           0\n",
       "M2.Middle.L    0\n",
       "K3.A           0\n",
       "K3.R           0\n",
       "dtype: float64"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "a.type.get_values(a.data, 'New.CleanUp.ReferenceOTU0')[:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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