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  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#First I need to download the file that SR has created from SQLshare"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "pyloc=\"/Applications/sqlshare-pythonclient-master/tools/\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!python {pyloc}fetchdata.py -d \"[sr320@washington.edu].[CGannot_Ensembl_feat]\" -f tsv -o /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/MasterFile/AllLoci.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Traceback (most recent call last):\r\n",
        "  File \"/Applications/sqlshare-pythonclient-master/tools/fetchdata.py\", line 76, in <module>\r\n",
        "    main()\r\n",
        "  File \"/Applications/sqlshare-pythonclient-master/tools/fetchdata.py\", line 71, in main\r\n",
        "    data = fetchdata(args.sql, args.format, args.output)\r\n",
        "  File \"/Applications/sqlshare-pythonclient-master/tools/fetchdata.py\", line 30, in fetchdata\r\n",
        "    return conn.download_sql_result(sql, format, output)\r\n",
        "  File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 337, in download_sql_result\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "    \r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 256, in poll_selector\r\n",
        "    \r\n",
        "  File \"/Users/claireolson/anaconda/lib/python2.7/httplib.py\", line 1045, in getresponse\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "    response.begin()\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  File \"/Users/claireolson/anaconda/lib/python2.7/httplib.py\", line 409, in begin\r\n",
        "    version, status, reason = self._read_status()\r\n",
        "  File \"/Users/claireolson/anaconda/lib/python2.7/httplib.py\", line 365, in _read_status\r\n",
        "    line = self.fp.readline(_MAXLINE + 1)\r\n",
        "  File \"/Users/claireolson/anaconda/lib/python2.7/socket.py\", line 476, in readline\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "    data = self._sock.recv(self._rbufsize)\r\n",
        "  File \"/Users/claireolson/anaconda/lib/python2.7/ssl.py\", line 241, in recv\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "    return self.read(buflen)\r\n",
        "  File \"/Users/claireolson/anaconda/lib/python2.7/ssl.py\", line 160, in read\r\n",
        "    return self._sslobj.read(len)\r\n",
        "socket.error: [Errno 54] Connection reset by peer\r\n"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
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}