QIIME 2 issue #190 example

qiime2-issue190.ipynb

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     "text": [
      "Running external command line application. This may print messages to stdout and/or stderr.\n",
      "The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.\n",
      "\n",
      "Command: FastTree -nt /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/qiime2-archive-wto551o4/aa4ef5af-050a-4cfc-a768-4fe59484f8d6/data/aligned-dna-sequences.fasta\n",
      "\n",
      "3f2db99e-ad89-4006-8dbe-4ede47775174\n"
     ]
    }
   ],
   "source": [
    "from qiime.plugins import phylogeny, alignment\n",
    "from q2_types import  FeatureData, AlignedSequence, Sequence\n",
    "import qiime\n",
    "\n",
    "aligned_seqs = qiime.Artifact.import_data(FeatureData[AlignedSequence], 'aligned-dna-sequences.fasta')\n",
    "\n",
    "# standard error goes to terminal where \"jupyter notebook\" is running\n",
    "tree = phylogeny.methods.fasttree(aligned_seqs)\n",
    "print(tree.tree.uuid)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Hello world!!\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "print(\"Hello world!!\", file=sys.stderr)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running external command line application. This may print messages to stdout and/or stderr.\n",
      "The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.\n",
      "\n",
      "Command: mafft --preservecase /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/qiime2-archive-rv181wqs/fddba98e-110d-41c1-b9c1-2748e384dfd9/data/dna-sequences.fasta\n",
      "\n",
      "84dacdc5-0104-4c7f-a2d5-4e0c847e5bf5\n"
     ]
    }
   ],
   "source": [
    "unaligned_seqs = qiime.Artifact.import_data(FeatureData[Sequence], 'dna-sequences.fasta')\n",
    "\n",
    "# standard error goes to terminal where \"jupyter notebook\" is running\n",
    "aln = alignment.methods.mafft(unaligned_seqs)\n",
    "print(aln.alignment.uuid)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Hello world!"
     ]
    }
   ],
   "source": [
    "sys.stderr.write('Hello world!')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "testing\r\n"
     ]
    }
   ],
   "source": [
    "!echo \"testing\" > /dev/stderr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">0\r\n",
      "ACGATCGAT--\r\n",
      ">1\r\n",
      "-CAGCTAGCAT\r\n"
     ]
    }
   ],
   "source": [
    "# for the sake of completeness\n",
    "!cat aligned-dna-sequences.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">0\r\n",
      "ACGATCGAT\r\n",
      ">1\r\n",
      "CAGCTAGCAT\r\n"
     ]
    }
   ],
   "source": [
    "# for the sake of completeness\n",
    "!cat dna-sequences.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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