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  "name": ""
 },
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  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Larvae Example Workflow- M1 Data (Spermatozoa from Male 1)"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "This is an example of my workflow for my bisulfite sequencing larvae dataset.  I am working with a total of 28 files and will narrow it down to a workflow of 7 datasets (1 female/eggs, 2 males/sperm, and 4 larvae samples)"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "1. Upload raw data to iPlant and unzip/uncompress this file this file using the gunzip analysis application"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6A781.png\" alt=\"_87__Discovery_Environment_18C6A781.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6A7B0.png\" alt=\"_87__Discovery_Environment_18C6A7B0.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "2. Dowload uncompressed files and relocate to Eagle"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "File locations for M1 uncompressed (Nov): http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FUncompressed_Nov%2F"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/Directory_Listing_of__Mollusk_bs_larvae_exp_Uncompressed_Nov_18C6A8BC.png\" alt=\"Directory_Listing_of__Mollusk_bs_larvae_exp_Uncompressed_Nov_18C6A8BC.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "3. Concatenate November and September uncompressed files (R1 and R2 separate).  These are technical replicates from the Bisulfite sequencing run."
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "M1_R1"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "M1_R2"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq "
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Location of concatenated files:"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "R1: http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FConcatenated_Files_R1%2F"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "R2: http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FConcatenated_Files_R2%2F"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "4. Upload these files to iPlant using the \"Import from URL\" function.  This allows me to import multiple files from the URL location on Eagle.  "
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AB07.png\" alt=\"_87__Discovery_Environment_18C6AB07.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "5. Run BSMAP in iPlant"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AD33.png\" alt=\"_87__Discovery_Environment_18C6AD33.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AD66.png\" alt=\"_87__Discovery_Environment_18C6AD66.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AD66.png\" alt=\"_87__Discovery_Environment_18C6AD66.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_93__Discovery_Environment_18C7E400.png\" alt=\"_93__Discovery_Environment_18C7E400.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "6. Download BSMAP files from iPlant and upload to Eagle "
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ir=\"/usr/local/bin/irods3.2.icmds.mac.intel/\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!{ir}/icd Larvae"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!icd /iplant/home/che625/Larvae/BSMAP"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_M1-2014-03-04-17-56-24.707/logs/condor-stdout-M1 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "7. Run methratio in iPython and filter for context and coverage"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#working directory (parent)\n",
      "wd=\"/Volumes/web/Mollusk/bs_larvae_exp\"\n",
      "\n",
      "#where is bsmap\n",
      "bsmap=\"/Users/Shared/Apps/bsmap-2.73/\"\n",
      "\n",
      "#Where is bsmap file\n",
      "bsmapfile=\"/Volumes/web/Mollusk/bs_larvae_exp/BSMAP_output/\"\n",
      "\n",
      "#Output for methratio file\n",
      "methratio=\"/Volumes/web/Mollusk/bs_larvae_exp/Methratio_out/\"\n",
      "\n",
      "#Location of filtered files\n",
      "filtered=\"/Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/\"\n",
      "\n",
      "#genome file \n",
      "genome=\"/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 33
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_M1.txt -s {bsmap}samtools {bsmapfile}condor-stdout-M1.sam"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Mar  5 15:42:06 2014: reading reference /Volumes/web-1/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Mar  5 15:43:41 2014: reading /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output/condor-stdout-M1.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\t@ Wed Mar  5 16:58:58 2014: read 10000000 lines\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Mar  5 17:00:08 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Mar  5 17:05:26 2014: writing /Volumes/web-1/Mollusk/bs_larvae_exp/Methratio_out/methratio_out_M1.txt ..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Mar  5 17:28:49 2014: done.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "total 8562480 valid mappings, 48969439 covered cytosines, average coverage: 1.80 fold.\r\n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#command for only obtaining the context '__CG_'\n",
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_M1.txt> {filtered}methratio_out_CG_M1.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#obtaining a filtered file with at least 5x coverage\n",
      "!awk '{if ($8 >= 5) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_M1.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 43
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!tr ' ' \"\\t\" </Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_M1_tab.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 44
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "8. Create a file formatted for visualization in IGV"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1,$2,$2+1,\"CpG\",$5}' /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_M1_tab.txt >/Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_IGV_M1.txt "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 45
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Second line of code for creating a formatted file for IGV\n",
      "!tr ' ' \"\\t\" </Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_IGV_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_IGV_M1.igv"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 46
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_IGV_M1.igv"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "C12768\t103\t104\tCpG\t0.167\r\n",
        "C12806\t142\t143\tCpG\t0.333\r\n",
        "C12924\t30\t31\tCpG\t0.000\r\n",
        "C12924\t38\t39\tCpG\t0.000\r\n",
        "C12924\t52\t53\tCpG\t0.000\r\n",
        "C12924\t60\t61\tCpG\t0.000\r\n",
        "C12924\t127\t128\tCpG\t0.000\r\n",
        "C12924\t136\t137\tCpG\t0.000\r\n",
        "C13128\t87\t88\tCpG\t0.000\r\n",
        "C13208\t83\t84\tCpG\t0.400\r\n"
       ]
      }
     ],
     "prompt_number": 47
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "9. Create a file formatted for visualization in the R package methylKit"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methratio_out_CG5x_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methylkit/methylkit_out_M1.txt "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 53
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Second line of code for creating a formatted file for methylKit\n",
      "!tr ' ' \"\\t\" </Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methylkit/methylkit_out_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methylkit/methylkit_out_M1b.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 54
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head /Volumes/web/Mollusk/bs_larvae_exp/Filtered_Larvae_Files/methylkit/methylkit_out_M1b.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "C12768\t103\t104\t+\t6\t0.166667\t0.833333\r\n",
        "C12806\t142\t143\t+\t6\t0.333333\t0.666667\r\n",
        "C12924\t30\t31\t+\t5\t0\t1\r\n",
        "C12924\t38\t39\t+\t5\t0\t1\r\n",
        "C12924\t52\t53\t+\t6\t0\t1\r\n",
        "C12924\t60\t61\t+\t6\t0\t1\r\n",
        "C12924\t127\t128\t+\t6\t0\t1\r\n",
        "C12924\t136\t137\t+\t6\t0\t1\r\n",
        "C13128\t87\t88\t+\t6\t0\t1\r\n",
        "C13208\t83\t84\t+\t5\t0.4\t0.6\r\n"
       ]
      }
     ],
     "prompt_number": 55
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Visualization of genomic tracks using IGV"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Comparison between samples using the R package methylKit"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%matplotlib inline"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%load_ext rmagic "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "ImportError",
       "evalue": "No module named rpy2.rinterface",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
        "\u001b[0;32m<ipython-input-2-67efefd52de2>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'load_ext rmagic'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m   2170\u001b[0m         \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2171\u001b[0m         \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2172\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2173\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2174\u001b[0m     \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m   2091\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2092\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2093\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2094\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2095\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/core/magics/extension.pyc\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    189\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 191\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    192\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    193\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/core/magics/extension.pyc\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     60\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mmodule_str\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     61\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mUsageError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Missing module name.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 62\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextension_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     63\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     64\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'already loaded'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/core/extensions.pyc\u001b[0m in \u001b[0;36mload_extension\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     96\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mmodule_str\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     97\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mprepended_to_syspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mipython_extension_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 98\u001b[0;31m                     \u001b[0m__import__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     99\u001b[0m             \u001b[0mmod\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    100\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_call_load_ipython_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/claireolson/anaconda/lib/python2.7/site-packages/IPython/extensions/rmagic.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     44\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     45\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 46\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mrpy2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrinterface\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mri\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     47\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mrpy2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrobjects\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mro\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;31mImportError\u001b[0m: No module named rpy2.rinterface"
       ]
      }
     ],
     "prompt_number": "*"
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Total number of loci for this comparison= 1126"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/RStudio_18CF9C36.png\" alt=\"RStudio_18CF9C36.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/RStudio_18CFA867.png\" alt=\"RStudio_18CFA867.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/RStudio_18CFA8C4.png\" alt=\"RStudio_18CFA8C4.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "The female/eggs are definitely an outlier.  I'm interested in comparing these samples excluding the Female from this analysis."
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Excluding eggs from the analysis the total number of loci for this comparison= 24193"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/RStudio_18CFAAF4.png\" alt=\"RStudio_18CFAAF4.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Male sperm samples are clustering with their respective larvae offspring"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/RStudio_18CFAB3D.png\" alt=\"RStudio_18CFAB3D.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/RStudio_18CFAB92.png\" alt=\"RStudio_18CFAB92.png\"/>"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}