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  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Tools"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "In developing qdod there are several handy tools for aggretating data. Here we will try to list them."
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Downloading data"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Section on how to get data automatically down from different resources including   \n",
      "\n",
      "- NCBI    \n",
      "- Ensembl    \n",
      "- Sigenae    \n"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "**Sqlshare** \n",
      "`!python {spd}fetchdata.py -s \"SELECT ProbeName,GB_ACC,Column2 as sequence,Description FROM [sr320@washington.edu].[GPL11353_array]ar left join [sr320@washington.edu].[Cgigas_EST__Nuc_NCBI_040414_cl]est on ar.GB_ACC=est.Column5\" -f tsv -o /Volumes/web/cnidarian/GPL11353_fasta2.tab`\n"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Uploading data"
     ]
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "#uploading to SQLSHARE\n",
      "spd=\"/Users/sr320/sqlshare-pythonclient/tools/\"\n",
      "!python {spd}singleupload.py -d Cgigas_EST_NCBI_040414_cl /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Manipulating "
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "**Fasta to tab**\n",
      "```\n",
      "!perl -e '$count=0; $len=0; while(<>) {s/\\r?\\n//; s/\\t/ /g; if (s/^>//) { if ($. != 1) {print \"\\n\"} s/ |$/\\t/; $count++; $_ .= \"\\t\";} else {s/ //g; $len += length($_)} print $_;} print \"\\n\"; warn \"\\nConverted $count FASTA records in $. lines to tabular format\\nTotal sequence length: $len\\n\\n\";' /Volumes/web/cnidarian/oyster.v9.fa > /Volumes/web/cnidarian/cgigas_v9_genome01.tab\n",
      "```"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "**Tab to fasta**\n",
      "`!awk -F \",\" '{print \">\"$1\"\\n\"$2}' /Volumes/web/cnidarian/GPL11353_v6fasta.csv > /Volumes/web/cnidarian/GPL11353_v6fasta.fa`"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}