fixed missing data in tables

caporaso-lab · Jun 29, 2015 · ef9014f · ef9014f
1 parent b60826d
commit ef9014f
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Showing 20 changed files with 521 additions and 11,513 deletions.
diff --git a/code/class.ipynb b/code/class.ipynb
diff --git a/code/family.ipynb b/code/family.ipynb
diff --git a/code/genus.ipynb b/code/genus.ipynb
diff --git a/code/order.ipynb b/code/order.ipynb
diff --git a/code/phylum.ipynb b/code/phylum.ipynb
diff --git a/code/species.ipynb b/code/species.ipynb
diff --git a/ipynb/mothur-evaluation/Index.ipynb b/ipynb/mothur-evaluation/Index.ipynb
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 12,
    "metadata": {
     "collapsed": false
    },
@@ -62,7 +62,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 13,
    "metadata": {
     "collapsed": true
    },
@@ -83,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 14,
    "metadata": {
     "collapsed": true
    },
@@ -94,23 +94,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 20,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "('',\n",
-       " '/usr/local/lib/python2.7/dist-packages/IPython/nbformat/current.py:19: UserWarning: IPython.nbformat.current is deprecated.\\n\\n- use IPython.nbformat for read/write/validate public API\\n- use IPython.nbformat.vX directly to composing notebooks of a particular version\\n\\n  \"\"\")\\nWARNING:root:Exiting with nonzero exit status\\n[NbConvertApp] Converting notebook /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/species-full.ipynb to notebook\\n[NbConvertApp] Writing 25515 bytes to species-full.ipynb\\n',\n",
-       " 0,\n",
-       " 'export taxonomic_level=7; export reference_choice=full-ref; cd /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation; runipy -q /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/base.ipynb /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/species-full.ipynb; ipython nbconvert --to notebook --nbformat 4 --inplace /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/species-full.ipynb')"
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "TimeoutError",
+     "evalue": "Result not ready.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mTimeoutError\u001b[0m                              Traceback (most recent call last)",
+      "\u001b[1;32m<ipython-input-20-e11c48483dcd>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mr\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[1;32m/usr/local/lib/python2.7/dist-packages/IPython/parallel/client/asyncresult.pyc\u001b[0m in \u001b[0;36m__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m    243\u001b[0m         \"\"\"\n\u001b[0;32m    244\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mint\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 245\u001b[1;33m             \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_check_ready\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    246\u001b[0m             \u001b[1;32mreturn\u001b[0m \u001b[0merror\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcollect_exceptions\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_result\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_fname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    247\u001b[0m         \u001b[1;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mslice\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;32m/usr/local/lib/python2.7/dist-packages/IPython/parallel/client/asyncresult.pyc\u001b[0m in \u001b[0;36m_check_ready\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m    108\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0m_check_ready\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    109\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mready\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 110\u001b[1;33m             \u001b[1;32mraise\u001b[0m \u001b[0merror\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mTimeoutError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"Result not ready.\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    111\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    112\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mready\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;31mTimeoutError\u001b[0m: Result not ready."
+     ]
     }
    ],
    "source": [
@@ -119,7 +119,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 17,
    "metadata": {
     "collapsed": false
    },
@@ -130,7 +130,7 @@
        "'export taxonomic_level=2; export reference_choice=partial-ref; cd /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation; runipy -q /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/base.ipynb /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/phylum-partial.ipynb; ipython nbconvert --to notebook --nbformat 4 --inplace /home/ubuntu/data/short-read-tax-assignment/ipynb/mothur-evaluation/phylum-partial.ipynb'"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }

diff --git a/ipynb/mothur-evaluation/base.ipynb b/ipynb/mothur-evaluation/base.ipynb
@@ -441,7 +441,7 @@
    "source": [
     "## OUTPUT RESULTS FOR YOUR NEW METHOD\n",
     "\n",
-    "mothur_top_params = parameter_comparisons(simulated_results, \"mothur\", metrics=['F-measure'])\n",
+    "mothur_top_params = parameter_comparisons(simulated_results, \"mothur\", metrics=metrics)\n",
     "mothur_top_params[:15]"
    ]
   },

diff --git a/ipynb/mothur-evaluation/class-full.ipynb b/ipynb/mothur-evaluation/class-full.ipynb
diff --git a/ipynb/mothur-evaluation/class-partial.ipynb b/ipynb/mothur-evaluation/class-partial.ipynb