{
 "metadata": {
  "name": "IntersectBed_IDTargetLoci",
  "signature": "sha256:aa3e2c1e465974cecd5bf14401def60e6c6b089d0387b00d08b61f58bbf50d91"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "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\n45 exon\n197 gene\n152 intron\n80 TE\n24 promoter\n214 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\n30 exon\n167 gene\n137 intron\n57 TE\n18 promoter\n176 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\nnb='IntersectBed_IDTargetLoci'\n\n#NOTEBOOK LOCATION\nnbloc='/Users/claireolson/Dropbox/Lab\\ \\(1\\)/IPython_nbs/Claire/'\n\n\n\n#TIMESTAMP\ndate=!date +%m%d_%H%M\n#LOCATION OF POST DIRECTORY\npost='/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": {}
  }
 ]
}