q2d3-test.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Prepare the environments with some imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from qiime.sdk.workflow import WorkflowTemplate\n",
    "from qiime.sdk.type.primitive import Int\n",
    "from feature_table import rarefy\n",
    "from feature_table.artifact_types.feature_table import FeatureTable, Frequency"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create an artifact to work with."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import biom\n",
    "from qiime.sdk.artifact import Artifact\n",
    "biom_path = \"/Users/caporaso/code/q2d2/example-data/keyboard/q191/otu-table.tsv\"\n",
    "\n",
    "table = biom.load_table(biom_path)\n",
    "Artifact.save(table, FeatureTable[Frequency], \"nothing...\", \"./table.qtf\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Instantiate the workflow template (note that the output is a concrete type here, so the fact that ``Signature.__call__`` isn't actually solving anything isn't a problem yet). "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "wt = WorkflowTemplate.from_function(function=rarefy, \n",
    "                                    inputs={'table': FeatureTable[Frequency], 'depth': Int}, \n",
    "                                    outputs={'rarefied_table': FeatureTable[Frequency]}, \n",
    "                                    name=\"Rarefaction\",\n",
    "                                    doc=\"Let's rarefy!\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Instantiate the context. Note that it discovers its artifacts."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from qiime.q2d3.context import Q2D3Context"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "q2d3 = Q2D3Context('./')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{UUID('3e8e39d1-f2b2-4428-b6e9-bd618093854e'): './table.qtf'}"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "q2d3.data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Call the context to generate the actual job. Here we're doing some ugly stuff to grab the UUID from ``q2d3.data``, since the UUID is different everytime we run this."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "```python\n",
      ">>> from qiime.sdk.artifact import Artifact\n",
      ">>> table = Artifact('./table.qtf').data\n",
      ">>> depth = 42\n",
      "```\n",
      "\n",
      "Let's rarefy!\n",
      "\n",
      "```python\n",
      ">>> from feature_table._normalize import rarefy\n",
      ">>> rarefied_table = rarefy(depth=depth, table=table)\n",
      "```\n",
      "\n",
      "```python\n",
      ">>> from feature_table.artifact_types.feature_table import Frequency\n",
      ">>> from feature_table.artifact_types.feature_table import FeatureTable\n",
      ">>> Artifact.save(rarefied_table, FeatureTable[Frequency], None, '/Users/caporaso/temp/q2d3-test/tmpmct3i3e_.qtf')\n",
      "```\n"
     ]
    }
   ],
   "source": [
    "print(q2d3(wt, {'table': list(q2d3.data.keys())[0]}, {'depth': 42}))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now, restart the kernel (see that the cell counts start over) and confirm that the job code does actually work. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from qiime.sdk.artifact import Artifact\n",
    "table = Artifact('./table.qtf').data\n",
    "depth = 42"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from feature_table._normalize import rarefy\n",
    "rarefied_table = rarefy(table=table, depth=depth)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from feature_table.artifact_types.feature_table import Frequency\n",
    "from feature_table.artifact_types.feature_table import FeatureTable\n",
    "Artifact.save(rarefied_table, FeatureTable[Frequency], None, '/Users/caporaso/temp/q2d3-test/tmpmct3i3e_.qtf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "x tmpmct3i3e_/\r\n",
      "x tmpmct3i3e_/metadata.yaml\r\n",
      "x tmpmct3i3e_/README.md\r\n",
      "x tmpmct3i3e_/data/\r\n",
      "x tmpmct3i3e_/data/feature-table.biom\r\n"
     ]
    }
   ],
   "source": [
    "!tar -xvf '/Users/caporaso/temp/q2d3-test/tmpmct3i3e_.qtf'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The table is rarefied! "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Num samples: 104\r\n",
      "Num observations: 340\r\n",
      "Total count: 4368\r\n",
      "Table density (fraction of non-zero values): 0.045\r\n",
      "\r\n",
      "Counts/sample summary:\r\n",
      " Min: 42.0\r\n",
      " Max: 42.0\r\n",
      " Median: 42.000\r\n",
      " Mean: 42.000\r\n",
      " Std. dev.: 0.000\r\n",
      " Sample Metadata Categories: None provided\r\n",
      " Observation Metadata Categories: taxonomy\r\n",
      "\r\n",
      "Counts/sample detail:\r\n",
      "M9.Pinky.R: 42.0\r\n",
      "K1.Shift.L: 42.0\r\n",
      "K3.G: 42.0\r\n",
      "M9.Pinky.L: 42.0\r\n",
      "K2.F: 42.0\r\n",
      "K3.Space: 42.0\r\n",
      "K3.Shift.L: 42.0\r\n",
      "K2.X: 42.0\r\n",
      "K3.P: 42.0\r\n",
      "K2.C: 42.0\r\n",
      "M9.Index.L: 42.0\r\n",
      "M2.Middle.R: 42.0\r\n",
      "K1.G: 42.0\r\n",
      "K3.O: 42.0\r\n",
      "K3.Enter: 42.0\r\n",
      "K2.P: 42.0\r\n",
      "M9.Thumb.L: 42.0\r\n",
      "M3.Index.L: 42.0\r\n",
      "K1.W: 42.0\r\n",
      "K3.J: 42.0\r\n",
      "K1.Y: 42.0\r\n",
      "K1.V: 42.0\r\n",
      "M2.Index.R: 42.0\r\n",
      "M3.Ring.L: 42.0\r\n",
      "K3.T: 42.0\r\n",
      "M2.Pinky.L: 42.0\r\n",
      "K1.R: 42.0\r\n",
      "K1.K: 42.0\r\n",
      "K3.K: 42.0\r\n",
      "K3.F: 42.0\r\n",
      "K3.Y: 42.0\r\n",
      "K1.H: 42.0\r\n",
      "K3.Z: 42.0\r\n",
      "K1.C: 42.0\r\n",
      "M3.Thumb.L: 42.0\r\n",
      "K3.W: 42.0\r\n",
      "M2.Thumb.R: 42.0\r\n",
      "M9.Index.R: 42.0\r\n",
      "M2.Index.L: 42.0\r\n",
      "K3.V: 42.0\r\n",
      "K3.X: 42.0\r\n",
      "K3.I: 42.0\r\n",
      "K2.Enter: 42.0\r\n",
      "M3.Ring.R: 42.0\r\n",
      "K2.O: 42.0\r\n",
      "K3.U: 42.0\r\n",
      "K2.A: 42.0\r\n",
      "K1.P: 42.0\r\n",
      "K2.Q: 42.0\r\n",
      "K3.Shift.R: 42.0\r\n",
      "K1.Space: 42.0\r\n",
      "M9.Middle.R: 42.0\r\n",
      "M3.Index.R: 42.0\r\n",
      "M2.Thumb.L: 42.0\r\n",
      "K1.T: 42.0\r\n",
      "K1.J: 42.0\r\n",
      "K2.S: 42.0\r\n",
      "K1.N: 42.0\r\n",
      "K1.E: 42.0\r\n",
      "K2.D: 42.0\r\n",
      "K1.A: 42.0\r\n",
      "K3.S: 42.0\r\n",
      "K3.R: 42.0\r\n",
      "K2.B: 42.0\r\n",
      "K3.D: 42.0\r\n",
      "K2.K: 42.0\r\n",
      "K3.H: 42.0\r\n",
      "K3.Q: 42.0\r\n",
      "K2.M: 42.0\r\n",
      "M3.Pinky.L: 42.0\r\n",
      "M9.Middle.L: 42.0\r\n",
      "K3.C: 42.0\r\n",
      "K2.W: 42.0\r\n",
      "K3.M: 42.0\r\n",
      "K1.B: 42.0\r\n",
      "K1.L: 42.0\r\n",
      "K3.L: 42.0\r\n",
      "K2.Space: 42.0\r\n",
      "M3.Middle.L: 42.0\r\n",
      "K3.B: 42.0\r\n",
      "K1.Q: 42.0\r\n",
      "M3.Pinky.R: 42.0\r\n",
      "K2.G: 42.0\r\n",
      "M9.Thumb.R: 42.0\r\n",
      "M9.Ring.R: 42.0\r\n",
      "M9.Ring.L: 42.0\r\n",
      "K3.E: 42.0\r\n",
      "K1.Shift.R: 42.0\r\n",
      "K1.Z: 42.0\r\n",
      "M2.Ring.L: 42.0\r\n",
      "K3.A: 42.0\r\n",
      "M2.Middle.L: 42.0\r\n",
      "K2.N: 42.0\r\n",
      "K2.V: 42.0\r\n",
      "M3.Middle.R: 42.0\r\n",
      "M2.Ring.R: 42.0\r\n",
      "K1.X: 42.0\r\n",
      "K1.M: 42.0\r\n",
      "M2.Pinky.R: 42.0\r\n",
      "K2.E: 42.0\r\n",
      "K3.N: 42.0\r\n",
      "K2.H: 42.0\r\n",
      "K2.Y: 42.0\r\n",
      "M3.Thumb.R: 42.0\r\n"
     ]
    }
   ],
   "source": [
    "!biom summarize-table -i tmpmct3i3e_/data/feature-table.biom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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