{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Re-defining canonical C gigas Genome Tracks"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "via Ensembl"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AA0C920.png\" alt=\"IGV_1AA0C920.png\"/>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "scaffold44098\tdust\trepeat_region\t518076\t518099\t.\t.\t.\tName=dust;class=dust;type=Dust\r\n",
      "scaffold44098\tdust\trepeat_region\t519261\t519281\t.\t.\t.\tName=dust;class=dust;type=Dust\r\n",
      "scaffold44098\ttrf\trepeat_region\t519261\t519281\t.\t.\t.\tName=trf;class=trf;repeat_consensus=AT;type=Tandem repeats\r\n"
     ]
    }
   ],
   "source": [
    "!tail -3 /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "186890 CDS\r\n",
      "   5 RNA\r\n",
      "189468 exon\r\n",
      "26114 gene\r\n",
      "  28 miRNA\r\n",
      "  28 miRNA_gene\r\n",
      "1410 pseudogenic_tRNA\r\n",
      "  13 rRNA\r\n",
      "  13 rRNA_gene\r\n",
      "875275 repeat_region\r\n",
      "  47 snRNA\r\n",
      "  47 snRNA_gene\r\n",
      "  20 snoRNA\r\n",
      "  20 snoRNA_gene\r\n",
      " 994 tRNA_gene\r\n",
      "28523 transcript\r\n"
     ]
    }
   ],
   "source": [
    "!cut -f 3 \\\n",
    "/Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   5 EnsemblGenomes\tRNA\r\n",
      "2530 EnsemblGenomes\texon\r\n",
      "  13 EnsemblGenomes\tgene\r\n",
      "  28 EnsemblGenomes\tmiRNA\r\n",
      "  28 EnsemblGenomes\tmiRNA_gene\r\n",
      "1410 EnsemblGenomes\tpseudogenic_tRNA\r\n",
      "  13 EnsemblGenomes\trRNA\r\n",
      "  13 EnsemblGenomes\trRNA_gene\r\n",
      "  47 EnsemblGenomes\tsnRNA\r\n",
      "  47 EnsemblGenomes\tsnRNA_gene\r\n",
      "  20 EnsemblGenomes\tsnoRNA\r\n",
      "  20 EnsemblGenomes\tsnoRNA_gene\r\n",
      " 994 EnsemblGenomes\ttRNA_gene\r\n",
      "2422 EnsemblGenomes\ttranscript\r\n",
      "186890 GigaDB\tCDS\r\n",
      "186938 GigaDB\texon\r\n",
      "26101 GigaDB\tgene\r\n",
      "26101 GigaDB\ttranscript\r\n",
      "650376 dust\trepeat_region\r\n",
      "224899 trf\trepeat_region\r\n"
     ]
    }
   ],
   "source": [
    "!cut -f 2,3 \\\n",
    "/Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "scaffold44098\tprotein_coding\tCDS\t509746\t510288\t.\t-\t0\t gene_id \"CGI_10017729\"; gene_version \"1\"; transcript_id \"EKC17988\"; transcript_version \"1\"; exon_number \"2\"; protein_id \"EKC17988\";\r\n",
      "scaffold44098\tprotein_coding\texon\t514550\t514690\t.\t-\t.\t gene_id \"CGI_10017729\"; gene_version \"1\"; transcript_id \"EKC17988\"; transcript_version \"1\"; exon_number \"1\"; seqedit \"false\";\r\n",
      "scaffold44098\tprotein_coding\tCDS\t514550\t514690\t.\t-\t0\t gene_id \"CGI_10017729\"; gene_version \"1\"; transcript_id \"EKC17988\"; transcript_version \"1\"; exon_number \"1\"; protein_id \"EKC17988\";\r\n",
      "scaffold44098\tprotein_coding\tstart_codon\t514688\t514690\t.\t-\t0\t gene_id \"CGI_10017729\"; gene_version \"1\"; transcript_id \"EKC17988\"; transcript_version \"1\"; exon_number \"1\";\r\n",
      "scaffold44098\tprotein_coding\texon\t514859\t515511\t.\t-\t.\t gene_id \"CGI_10017730\"; gene_version \"1\"; transcript_id \"EKC17989\"; transcript_version \"1\"; exon_number \"2\"; seqedit \"false\";\r\n",
      "scaffold44098\tprotein_coding\tstop_codon\t514859\t514861\t.\t-\t0\t gene_id \"CGI_10017730\"; gene_version \"1\"; transcript_id \"EKC17989\"; transcript_version \"1\"; exon_number \"2\";\r\n",
      "scaffold44098\tprotein_coding\tCDS\t514862\t515511\t.\t-\t2\t gene_id \"CGI_10017730\"; gene_version \"1\"; transcript_id \"EKC17989\"; transcript_version \"1\"; exon_number \"2\"; protein_id \"EKC17989\";\r\n",
      "scaffold44098\tprotein_coding\texon\t515871\t515877\t.\t-\t.\t gene_id \"CGI_10017730\"; gene_version \"1\"; transcript_id \"EKC17989\"; transcript_version \"1\"; exon_number \"1\"; seqedit \"false\";\r\n",
      "scaffold44098\tprotein_coding\tCDS\t515871\t515877\t.\t-\t0\t gene_id \"CGI_10017730\"; gene_version \"1\"; transcript_id \"EKC17989\"; transcript_version \"1\"; exon_number \"1\"; protein_id \"EKC17989\";\r\n",
      "scaffold44098\tprotein_coding\tstart_codon\t515875\t515877\t.\t-\t0\t gene_id \"CGI_10017730\"; gene_version \"1\"; transcript_id \"EKC17989\"; transcript_version \"1\"; exon_number \"1\";\r\n"
     ]
    }
   ],
   "source": [
    "!tail /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gtf"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   2 RNase_MRP_RNA\texon\r\n",
      "   1 RNase_P_RNA\texon\r\n",
      "  10 SRP_RNA\texon\r\n",
      "  28 miRNA\texon\r\n",
      "   5 misc_RNA\texon\r\n",
      "  48 nontranslating_CDS\texon\r\n",
      "186890 protein_coding\tCDS\r\n",
      "186890 protein_coding\texon\r\n",
      "25587 protein_coding\tstart_codon\r\n",
      "26087 protein_coding\tstop_codon\r\n",
      "  13 rRNA\texon\r\n",
      "  47 snRNA\texon\r\n",
      "  20 snoRNA\texon\r\n",
      " 994 tRNA\texon\r\n",
      "1410 tRNA_pseudogene\texon\r\n"
     ]
    }
   ],
   "source": [
    "!cut -f 2,3 \\\n",
    "/Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gtf \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# via GigaDB aka version9"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff <==\r\n",
      "scaffold999\tflankbed\tpromoter\t99703\t100702\t.\t-\t.\tID=CGI_10006972;\r",
      "\r\n",
      "scaffold999\tflankbed\tpromoter\t106744\t107743\t.\t+\t.\tID=CGI_10006973;\r",
      "\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff <==\r\n",
      "scaffold38980\tfuzznuc\tnucleotide_motif\t63903\t63904\t2\t+\t.\tID=scaffold38980.744;note=*pat pattern:CG\r\n",
      "scaffold38980\tfuzznuc\tnucleotide_motif\t64051\t64052\t2\t+\t.\tID=scaffold38980.745;note=*pat pattern:CG\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-TANDEMREPEAT.gff <==\r\n",
      "scaffold999\tTRF\tTandem_Repeat\t153009\t153196\t189\t+\t.\t.\r\n",
      "scaffold999\tTRF\tTandem_Repeat\t166754\t166792\t69\t+\t.\t.\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff <==\r\n",
      "scaffold1009\tWUBlastX\tDNA_TcMar-Tc2\t1790325\t1790603\t20\t+\t.\t.\r\n",
      "scaffold983\tWUBlastX\tDNA_TcMar-Tc1\t369636\t369770\t26\t-\t.\t.\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff <==\r\n",
      "scaffold1009\tWUBlastX\tDNA_TcMar-Tc2\t1790325\t1790603\t20\t+\t.\t.\r\n",
      "scaffold983\tWUBlastX\tDNA_TcMar-Tc1\t369636\t369770\t26\t-\t.\t.\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TEx.gff <==\r\n",
      "scaffold1009\tWUBlastX\tDNA_TcMar-Tc2\t1790325\t1790603\t20\t+\t.\t.\r\n",
      "scaffold983\tWUBlastX\tDNA_TcMar-Tc1\t369636\t369770\t26\t-\t.\t.\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff <==\r\n",
      "scaffold22\tGLEAN\tCDS\t1870289\t1870360\t.\t-\t0\tParent=CGI_10028939;\r\n",
      "scaffold22\tGLEAN\tCDS\t1869336\t1869428\t.\t-\t0\tParent=CGI_10028939;\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff <==\r\n",
      "scaffold22\tGLEAN\tmRNA\t1863760\t1864161\t0.544455\t+\t.\tID=CGI_10028938;\r\n",
      "scaffold22\tGLEAN\tmRNA\t1869336\t1885890\t0.999933\t-\t.\tID=CGI_10028939;\r\n",
      "\r\n",
      "==> /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff <==\r\n",
      "scaffold999\tsubtractBed\tintrn\t124997\t126011\t.\t+\t.\tParent=CGI_10006973;\r",
      "\r\n",
      "scaffold999\tsubtractBed\tintrn\t126144\t126616\t.\t+\t.\tParent=CGI_10006973;\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!tail -2 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_*.gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   28023 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff\n",
      " 10035701 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff\n",
      "   61319 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-TANDEMREPEAT.gff\n",
      "   58468 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff\n",
      "  119786 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff\n",
      "   58468 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TEx.gff\n",
      "  196691 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff\n",
      "   28027 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff\n",
      "  176049 /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff\n",
      " 10762532 total\n"
     ]
    }
   ],
   "source": [
    "!wc -l /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_*.gff"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1AA0D065.png\" alt=\"IGV_1AA0D065.png\"/>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Comparison"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Array-feature-overlap-02_1AA0D233.png\" alt=\"Array-feature-overlap-02_1AA0D233.png\"/>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Lets see if can take all array and intersect with Ensembl gff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1373 GigaDB\tCDS\r\n",
      "1373 GigaDB\texon\r\n",
      "8468 GigaDB\tgene\r\n",
      "8468 GigaDB\ttranscript\r\n",
      "1240 dust\trepeat_region\r\n",
      " 975 trf\trepeat_region\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3 \\\n",
    "| cut -f 6,7 \\\n",
    "| sort | uniq -c | sed '/#/d'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   2 EnsemblGenomes\texon\r\n",
      "   1 EnsemblGenomes\tpseudogenic_tRNA\r\n",
      "   1 EnsemblGenomes\ttRNA_gene\r\n",
      "   2 EnsemblGenomes\ttranscript\r\n",
      "1177 GigaDB\tCDS\r\n",
      "1177 GigaDB\texon\r\n",
      "8491 GigaDB\tgene\r\n",
      "8491 GigaDB\ttranscript\r\n",
      "1320 dust\trepeat_region\r\n",
      " 873 trf\trepeat_region\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3 \\\n",
    "| cut -f 6,7 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   1 EnsemblGenomes\texon\r\n",
      "   1 EnsemblGenomes\tsnRNA\r\n",
      "   1 EnsemblGenomes\tsnRNA_gene\r\n",
      " 947 GigaDB\tCDS\r\n",
      " 948 GigaDB\texon\r\n",
      "9689 GigaDB\tgene\r\n",
      "9689 GigaDB\ttranscript\r\n",
      "1591 dust\trepeat_region\r\n",
      " 864 trf\trepeat_region\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3 \\\n",
    "| cut -f 6,7 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   5 EnsemblGenomes\tRNA\r\n",
      " 444 EnsemblGenomes\texon\r\n",
      "   6 EnsemblGenomes\tgene\r\n",
      "   2 EnsemblGenomes\tmiRNA\r\n",
      "   2 EnsemblGenomes\tmiRNA_gene\r\n",
      " 259 EnsemblGenomes\tpseudogenic_tRNA\r\n",
      "  14 EnsemblGenomes\tsnRNA\r\n",
      "  14 EnsemblGenomes\tsnRNA_gene\r\n",
      "   6 EnsemblGenomes\tsnoRNA\r\n",
      "   6 EnsemblGenomes\tsnoRNA_gene\r\n",
      " 152 EnsemblGenomes\ttRNA_gene\r\n",
      " 422 EnsemblGenomes\ttranscript\r\n",
      "157279 GigaDB\tCDS\r\n",
      "157307 GigaDB\texon\r\n",
      "600445 GigaDB\tgene\r\n",
      "600445 GigaDB\ttranscript\r\n",
      "56210 dust\trepeat_region\r\n",
      "42390 trf\trepeat_region\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/array-design/OID40453_probe_locations.gff \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.sorted.gff3 \\\n",
    "| cut -f 11,12 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# TEs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 383 WUBlastX\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff \\\n",
    "| cut -f 6 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 254 WUBlastX\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff \\\n",
    "| cut -f 6 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 168 WUBlastX\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff \\\n",
    "| cut -f 6 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "10322 WUBlastX\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/array-design/OID40453_probe_locations.gff \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff \\\n",
    "| cut -f 11 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Promoters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 976 flankbed\tpromoter\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \\\n",
    "| cut -f 6,7 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 992 flankbed\tpromoter\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \\\n",
    "| cut -f 6,7 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1248 flankbed\tpromoter\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \\\n",
    "| cut -f 6,7 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "66368 flankbed\r\n"
     ]
    }
   ],
   "source": [
    "!intersectbed \\\n",
    "-wb \\\n",
    "-a /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/array-design/OID40453_probe_locations.gff \\\n",
    "-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \\\n",
    "| cut -f 11 \\\n",
    "| sort | uniq -c | sed '/#/d'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Plot"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Book_1AA0DEB2.png\" alt=\"Book_1AA0DEB2.png\"/>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "oys2\toys4\toys6\tProbes\n",
    "gene\t8468\t8491\t9689\t600445\n",
    "exon\t1373\t1177\t948\t157307\n",
    "intron\t7095\t7314\t8741\t443138\n",
    "dust repeat\t1240\t1320\t1591\t56210\n",
    "trf repeat\t975\t873\t864\t42390\n",
    "TE-blast\t383\t254\t168\t10322\n",
    "promoter\t976\t992\t1248\t66368\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "# Analysis of one proportion"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "http://nbviewer.ipython.org/github/thomas-haslwanter/statsintro/blob/master/ipynb/70_compGroups.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Populating the interactive namespace from numpy and matplotlib\n"
     ]
    }
   ],
   "source": [
    "%pylab inline\n",
    "import scipy.stats as stats"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ONE PROPORTION\n",
      "The confidence interval for the given sample is 0.224 to 0.226\n"
     ]
    }
   ],
   "source": [
    "# Get the data Probes exon\n",
    "numTotal = 697753\n",
    "numPositive = 157307\n",
    "\n",
    "# Calculate the confidence intervals\n",
    "p = float(numPositive)/numTotal\n",
    "se = sqrt(p*(1-p)/numTotal)\n",
    "td = stats.t(numTotal-1)\n",
    "ci = p + array([-1,1])*td.isf(0.025)*se\n",
    "\n",
    "# Print them\n",
    "print('ONE PROPORTION')\n",
    "print('The confidence interval for the given sample is {0:5.3f} to {1:5.3f}'.format(\n",
    "    ci[0], ci[1]))\n",
    " "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Chi-square test to a 2x2 table\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CHI SQUARE\n",
      "The corrected chi2 value is 47.663, with p=0.000\n",
      "The uncorrected chi2 value is 47.772, with p=0.000\n"
     ]
    }
   ],
   "source": [
    "# Enter the data comparing Oyster 2; probes at intron\n",
    "obs = array([[7095, 10028], [443138, 697753]])\n",
    "\n",
    "# Calculate the chi-square test\n",
    "chi2_corrected = stats.chi2_contingency(obs, correction=True)\n",
    "chi2_uncorrected = stats.chi2_contingency(obs, correction=False)\n",
    "\n",
    "# Print the result\n",
    "print('CHI SQUARE')\n",
    "print('The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'.format(chi2_corrected[0], chi2_corrected[1]))\n",
    "print('The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'.format(chi2_uncorrected[0], chi2_uncorrected[1]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CHI SQUARE\n",
      "The corrected chi2 value is 1.597, with p=0.206\n",
      "The uncorrected chi2 value is 1.616, with p=0.204\n"
     ]
    }
   ],
   "source": [
    "# Enter the data comparing Oyster 2; probes at gene\n",
    "obs = array([[8468, 10028], [600445, 697753]])\n",
    "\n",
    "# Calculate the chi-square test\n",
    "chi2_corrected = stats.chi2_contingency(obs, correction=True)\n",
    "chi2_uncorrected = stats.chi2_contingency(obs, correction=False)\n",
    "\n",
    "# Print the result\n",
    "print('CHI SQUARE')\n",
    "print('The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'.format(chi2_corrected[0], chi2_corrected[1]))\n",
    "print('The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'.format(chi2_uncorrected[0], chi2_uncorrected[1]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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