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  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Using the intersectBed function to classify our target loci with respect to oyster genomic regions"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd /Users/Shared/Apps/bedtools-2.17.0 "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Users/Shared/Apps/bedtools-2.17.0\n"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd bin"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Users/Shared/Apps/bedtools-2.17.0/bin\n"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_exon.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_exon.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      45     180    1685 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_exon.txt\r\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_gene.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_gene.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     197     788    7398 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_gene.txt\r\n"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_intron.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_intron.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     152     608    5713 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_intron.txt\r\n"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 59
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      80     320    2988 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE.txt\r\n"
       ]
      }
     ],
     "prompt_number": 60
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_promoter.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 16
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_promoter.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      24      96     910 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_promoter.txt\r\n"
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_COMP.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_COMP.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     214     856    7808 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_COMP.txt\r\n"
       ]
      }
     ],
     "prompt_number": 20
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "Lineage specific counts\n",
      "45 exon\n",
      "197 gene\n",
      "152 intron\n",
      "80 TE\n",
      "24 promoter\n",
      "214 complement (other)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_exon.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 21
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_exon.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      30     120    1061 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_exon.txt\r\n"
       ]
      }
     ],
     "prompt_number": 22
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_gene.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_gene.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     167     668    5976 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_gene.txt\r\n"
       ]
      }
     ],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_intron.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_intron.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     137     548    4915 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_intron.txt\r\n"
       ]
      }
     ],
     "prompt_number": 26
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 27
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      57     228    1983 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE.txt\r\n"
       ]
      }
     ],
     "prompt_number": 28
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_1k5p_gene_promoter.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_promoter.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      18      72     634 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_1k5p_gene_promoter.txt\r\n"
       ]
      }
     ],
     "prompt_number": 30
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_COMP.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 32
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_COMP.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     176     704    6052 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_COMP.txt\r\n"
       ]
      }
     ],
     "prompt_number": 33
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "Developmentally different counts\n",
      "30 exon\n",
      "167 gene\n",
      "137 intron\n",
      "57 TE\n",
      "18 promoter\n",
      "176 complement (other)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_exon.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 34
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_exon.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 1129658 11296580 110957829 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_exon.txt\r\n"
       ]
      }
     ],
     "prompt_number": 35
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_gene.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 36
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_gene.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 3938356 39383560 387141916 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_gene.txt\r\n"
       ]
      }
     ],
     "prompt_number": 37
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_intron.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 38
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_intron.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 2815997 28159970 276901690 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_intron.txt\r\n"
       ]
      }
     ],
     "prompt_number": 39
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 72
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  589509 5895090 57596188 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE.txt\r\n"
       ]
      }
     ],
     "prompt_number": 73
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_promoter.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 42
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_promoter.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  593081 5930810 58106466 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_promoter.txt\r\n"
       ]
      }
     ],
     "prompt_number": 43
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_COMP.txt -u"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 46
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_COMP.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 5121236 51212360 499097421 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_COMP.txt\r\n"
       ]
      }
     ],
     "prompt_number": 47
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE_names.txt -wb"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 57
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE_names.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     112    1456   10347 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE_names.txt\r\n"
       ]
      }
     ],
     "prompt_number": 58
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE_names.txt -wb"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 69
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE_names.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      88    1144    7777 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE_names.txt\r\n"
       ]
      }
     ],
     "prompt_number": 70
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE_names.txt -wb"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 75
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE_names.txt "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "wc: /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE_names.txt: open: No such file or directory\r\n"
       ]
      }
     ],
     "prompt_number": 74
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#NOTEBOOK NAME\n",
      "nb='IntersectBed_IDTargetLoci'\n",
      "\n",
      "#NOTEBOOK LOCATION\n",
      "nbloc='/Users/claireolson/Dropbox/Lab\\ \\(1\\)/IPython_nbs/Claire/'\n",
      "\n",
      "\n",
      "\n",
      "#TIMESTAMP\n",
      "date=!date +%m%d_%H%M\n",
      "#LOCATION OF POST DIRECTORY\n",
      "post='/Volumes/web/Mollusk/iPython_Posts/'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd {post}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/Mollusk/iPython_Posts\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/IntersectBed_IDTargetLoci.ipynb to html\r\n",
        "[NbConvertApp] Support files will be in IntersectBed_IDTargetLoci[0718_1218]_files/\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Loaded template html_full.tpl\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Writing 223480 bytes to IntersectBed_IDTargetLoci[0718_1218].html\r\n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}