{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Genomic Location of DML"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In this notebook, I will identify the genomic locations of [DML identified with `methylKit`](https://github.com/RobertsLab/project-oyster-oa/blob/master/code/Haws/04-methylKit.R). \n",
    "\n",
    "2. Create BEDfiles for DML\n",
    "4. Identify overlaps between pH- and ploidy-DML\n",
    "3. Characterize genomic locations for DML\n",
    "5. Identify overlaps between SNPs and DML"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 0. Set working directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/yaaminivenkataraman/Documents/project-oyster-oa/code/Haws'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/yaaminivenkataraman/Documents/project-oyster-oa/analyses\n"
     ]
    }
   ],
   "source": [
    "cd ../../analyses/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#mkdir Haws_07-DML-characterization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/yaaminivenkataraman/Documents/project-oyster-oa/analyses/Haws_07-DML-characterization\n"
     ]
    }
   ],
   "source": [
    "cd Haws_07-DML-characterization/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/opt/homebrew/bin/intersectBed\r\n"
     ]
    }
   ],
   "source": [
    "!which intersectBed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "bedtoolsDirectory = \"/opt/homebrew/bin/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Create BEDfiles for DML"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "My DML lists are `.csv` files. To identify genomic locations with `bedtools intersect`, I need BEDfiles."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ",chr,start,end,strand,pvalue,qvalue,meth.diff\r\n",
      "49125,NC_047559.1,5294172,5294174,*,6.81863140326384e-14,8.40451241428843e-08,40.2560083594566\r\n",
      "885150,NC_047560.1,65604843,65604845,*,3.34714016321879e-07,0.00946585966971852,49.4839101396478\r\n",
      "888648,NC_047560.1,66080783,66080785,*,2.24994610517064e-07,0.00775731411903371,-51.6483516483517\r\n",
      "923332,NC_047560.1,72583152,72583154,*,6.60249993674503e-23,1.62762259467936e-16,-40\r\n",
      "1008760,NC_047561.1,7843128,7843130,*,5.49971909095006e-08,0.0032137058072851,-26.3157894736842\r\n",
      "1035367,NC_047561.1,10147466,10147468,*,5.73605741393552e-08,0.0032137058072851,-30.4647676161919\r\n",
      "1035580,NC_047561.1,10166213,10166215,*,1.68763140575909e-09,0.000393983826907299,-29.1507066437723\r\n",
      "1047890,NC_047561.1,11783086,11783088,*,1.4461592764831e-09,0.000393983826907299,-44.1576698155646\r\n",
      "1103577,NC_047561.1,16521359,16521361,*,1.50728082250528e-09,0.000393983826907299,28.8444735692442\r\n"
     ]
    }
   ],
   "source": [
    "#Look at csv file to determine what modifications need to be made\n",
    "#Column 2: chr, Column 3: start, Column 4: end, Column 8: meth.diff\n",
    "!head ../Haws_04-methylKit/DML/DML-pH-25-Cov5.csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "../Haws_04-methylKit/DML/DML-pH-25-Cov5.csv\r\n",
      "../Haws_04-methylKit/DML/DML-ploidy-25-Cov5.csv\r\n"
     ]
    }
   ],
   "source": [
    "#Will use 25% meth diff cutoff for DML definition\n",
    "!find ../Haws_04-methylKit/DML/DML*25*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "\n",
    "#Replace , with tabs\n",
    "#Remove extraneous quotes entries (can also be done in R)\n",
    "#Print chr, start, end, meth.diff\n",
    "#Remove header\n",
    "#Save as BEDfile\n",
    "\n",
    "for f in ../Haws_04-methylKit/DML/DML*25*\n",
    "do\n",
    "    tr \",\" \"\\t\" < ${f} \\\n",
    "    | awk '{print $2\"\\t\"$3\"\\t\"$4\"\\t\"$8}' \\\n",
    "    | tail -n+2 \\\n",
    "    > ${f}.bed\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "\n",
    "#Move BEDfiles to current working directory\n",
    "mv ../Haws_04-methylKit/DML/*bed ."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "==> DML-pH-25-Cov5.csv.bed <==\r\n",
      "NC_047559.1\t5294172\t5294174\t40.2560083594566\r\n",
      "NC_047560.1\t65604843\t65604845\t49.4839101396478\r\n",
      "NC_047560.1\t66080783\t66080785\t-51.6483516483517\r\n",
      "NC_047560.1\t72583152\t72583154\t-40\r\n",
      "NC_047561.1\t7843128\t7843130\t-26.3157894736842\r\n",
      "NC_047561.1\t10147466\t10147468\t-30.4647676161919\r\n",
      "NC_047561.1\t10166213\t10166215\t-29.1507066437723\r\n",
      "NC_047561.1\t11783086\t11783088\t-44.1576698155646\r\n",
      "NC_047561.1\t16521359\t16521361\t28.8444735692442\r\n",
      "NC_047561.1\t19286180\t19286182\t-55.4137931034483\r\n",
      "\r\n",
      "==> DML-ploidy-25-Cov5.csv.bed <==\r\n",
      "NC_047559.1\t12799610\t12799612\t27.7297297297297\r\n",
      "NC_047559.1\t22468723\t22468725\t28.4117647058823\r\n",
      "NC_047559.1\t44801744\t44801746\t34.0988480118915\r\n",
      "NC_047559.1\t53732861\t53732863\t25.8426966292135\r\n",
      "NC_047561.1\t9365798\t9365800\t34.0129358830146\r\n",
      "NC_047561.1\t28489237\t28489239\t-25.6018518518519\r\n",
      "NC_047561.1\t40362698\t40362700\t29.4117647058824\r\n",
      "NC_047563.1\t39926052\t39926054\t42.6872058194266\r\n",
      "NC_047564.1\t23049738\t23049740\t29.2845880961766\r\n",
      "NC_047564.1\t24426622\t24426624\t-30.0865800865801\r\n"
     ]
    }
   ],
   "source": [
    "!head *bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\n",
      "       1 DML-Cov5-Overlaps.bed\n"
     ]
    }
   ],
   "source": [
    "#Find overlaps between pH- and ploidy-DML\n",
    "#Check head\n",
    "#Count number of overlapping DML\n",
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5.csv.bed \\\n",
    "-b DML-ploidy-25-Cov5.csv.bed \\\n",
    "> DML-Cov5-Overlaps.bed\n",
    "!head DML-Cov5-Overlaps.bed\n",
    "!wc -l DML-Cov5-Overlaps.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "I imported the BEDfiles into [this IGV session]() to visualize them."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## 2. SNP overlap"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I will now look at overlaps between DML and unique C->T SNPs. After quantifying the number of SNPs in each DML list, I'll remove them for downstream analyses."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2a. Create BEDfiles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_001276.1\t12440\t.\tC\tT\r\n",
      "NC_001276.1\t7226\t.\tC\tT\r\n",
      "NC_047559.1\t10001065\t.\tC\tT\r\n",
      "NC_047559.1\t10001128\t.\tC\tT\r\n",
      "NC_047559.1\t1000226\t.\tC\tT\r\n",
      "NC_047559.1\t10004318\t.\tC\tT\r\n",
      "NC_047559.1\t100045\t.\tC\tT\r\n",
      "NC_047559.1\t10004558\t.\tC\tT\r\n",
      "NC_047559.1\t10005322\t.\tC\tT\r\n",
      "NC_047559.1\t10005684\t.\tC\tT\r\n"
     ]
    }
   ],
   "source": [
    "!head /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.tab"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_001276.1\t12440\t12440\r\n",
      "NC_001276.1\t7226\t7226\r\n",
      "NC_047559.1\t10001065\t10001065\r\n",
      "NC_047559.1\t10001128\t10001128\r\n",
      "NC_047559.1\t1000226\t1000226\r\n",
      "NC_047559.1\t10004318\t10004318\r\n",
      "NC_047559.1\t100045\t100045\r\n",
      "NC_047559.1\t10004558\t10004558\r\n",
      "NC_047559.1\t10005322\t10005322\r\n",
      "NC_047559.1\t10005684\t10005684\r\n"
     ]
    }
   ],
   "source": [
    "!awk '{print $1\"\\t\"$2\"\\t\"$2}' /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.tab \\\n",
    "> /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.bed\n",
    "!head /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2b. Overlaps with Unique C/T SNPs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047560.1\t65604843\t65604845\t49.4839101396478\n",
      "NC_047561.1\t7843128\t7843130\t-26.3157894736842\n",
      "NC_047561.1\t10166213\t10166215\t-29.1507066437723\n",
      "NC_047561.1\t39008886\t39008888\t-35.8974358974359\n",
      "NC_047567.1\t15896903\t15896905\t-28.3455405508507\n",
      "NC_047568.1\t46593770\t46593772\t-26.1194029850746\n",
      "       6 DML-pH-25-Cov5-unique-CT-SNPs.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5.csv.bed \\\n",
    "-b /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.bed \\\n",
    "> DML-pH-25-Cov5-unique-CT-SNPs.bed\n",
    "!head DML-pH-25-Cov5-unique-CT-SNPs.bed\n",
    "!wc -l DML-pH-25-Cov5-unique-CT-SNPs.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t22468723\t22468725\t28.4117647058823\n",
      "NC_047559.1\t44801744\t44801746\t34.0988480118915\n",
      "NC_047561.1\t28489237\t28489239\t-25.6018518518519\n",
      "NC_047565.1\t11970715\t11970717\t46.6938636749958\n",
      "NC_047568.1\t46583284\t46583286\t-33.1582332761578\n",
      "       5 DML-ploidy-25-Cov5-unique-CT-SNPs.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5.csv.bed \\\n",
    "-b /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.bed \\\n",
    "> DML-ploidy-25-Cov5-unique-CT-SNPs.bed\n",
    "!head DML-ploidy-25-Cov5-unique-CT-SNPs.bed\n",
    "!wc -l DML-ploidy-25-Cov5-unique-CT-SNPs.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-unique-CT-SNPs.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps.bed \\\n",
    "-b /Volumes/web/spartina/project-oyster-oa/Haws/BS-Snper/unique-CT-SNPs.bed \\\n",
    "> DML-Cov5-Overlaps-unique-CT-SNPs.bed\n",
    "!head DML-Cov5-Overlaps-unique-CT-SNPs.bed\n",
    "!wc -l DML-Cov5-Overlaps-unique-CT-SNPs.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2c. Remove C->T SNPs from DML lists"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t5294172\t5294174\t40.2560083594566\n",
      "NC_047560.1\t66080783\t66080785\t-51.6483516483517\n",
      "NC_047560.1\t72583152\t72583154\t-40\n",
      "NC_047561.1\t10147466\t10147468\t-30.4647676161919\n",
      "NC_047561.1\t11783086\t11783088\t-44.1576698155646\n",
      "NC_047561.1\t16521359\t16521361\t28.8444735692442\n",
      "NC_047561.1\t19286180\t19286182\t-55.4137931034483\n",
      "NC_047561.1\t19545407\t19545409\t-41.4451612903226\n",
      "NC_047561.1\t21915577\t21915579\t46.9271523178808\n",
      "NC_047561.1\t31290734\t31290736\t-30.2791262135922\n",
      "      34 DML-pH-25-Cov5-NO-SNPs.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}subtractBed \\\n",
    "-a DML-pH-25-Cov5.csv.bed \\\n",
    "-b DML-pH-25-Cov5-unique-CT-SNPs.bed \\\n",
    "> DML-pH-25-Cov5-NO-SNPs.bed\n",
    "!head DML-pH-25-Cov5-NO-SNPs.bed\n",
    "!wc -l DML-pH-25-Cov5-NO-SNPs.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t12799610\t12799612\t27.7297297297297\n",
      "NC_047559.1\t53732861\t53732863\t25.8426966292135\n",
      "NC_047561.1\t9365798\t9365800\t34.0129358830146\n",
      "NC_047561.1\t40362698\t40362700\t29.4117647058824\n",
      "NC_047563.1\t39926052\t39926054\t42.6872058194266\n",
      "NC_047564.1\t23049738\t23049740\t29.2845880961766\n",
      "NC_047564.1\t24426622\t24426624\t-30.0865800865801\n",
      "NC_047564.1\t25380708\t25380710\t-40.1414677276746\n",
      "NC_047565.1\t10523508\t10523510\t38.0689469431726\n",
      "NC_047565.1\t13203393\t13203395\t41.1725955204216\n",
      "      24 DML-ploidy-25-Cov5-NO-SNPs.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}subtractBed \\\n",
    "-a DML-ploidy-25-Cov5.csv.bed \\\n",
    "-b DML-ploidy-25-Cov5-unique-CT-SNPs.bed \\\n",
    "> DML-ploidy-25-Cov5-NO-SNPs.bed\n",
    "!head DML-ploidy-25-Cov5-NO-SNPs.bed\n",
    "!wc -l DML-ploidy-25-Cov5-NO-SNPs.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\n",
      "       1 DML-Cov5-Overlaps-NO-SNPs.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}subtractBed \\\n",
    "-a DML-Cov5-Overlaps.bed \\\n",
    "-b DML-Cov5-Overlaps-unique-CT-SNPs.bed \\\n",
    "> DML-Cov5-Overlaps-NO-SNPs.bed\n",
    "!head DML-Cov5-Overlaps-NO-SNPs.bed\n",
    "!wc -l DML-Cov5-Overlaps-NO-SNPs.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Characterize SNP-free DML lists"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      24\n",
      "      10\n"
     ]
    }
   ],
   "source": [
    "#Count hypomethylated DML\n",
    "#Count hypermethylated DML\n",
    "!grep \"-\" DML-pH-25-Cov5-NO-SNPs.bed | wc -l\n",
    "!grep -v \"-\" DML-pH-25-Cov5-NO-SNPs.bed | wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       8\n",
      "      16\n"
     ]
    }
   ],
   "source": [
    "#Count hypomethylated DML\n",
    "#Count hypermethylated DML\n",
    "!grep \"-\" DML-ploidy-25-Cov5-NO-SNPs.bed | wc -l\n",
    "!grep -v \"-\" DML-ploidy-25-Cov5-NO-SNPs.bed | wc -l"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4. Characterize genomic locations of DML"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "I will look at overlaps between genome features and either pH- or ploidy-DML."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4a. Gene"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### pH"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t5294172\t5294174\t40.2560083594566\n",
      "NC_047560.1\t72583152\t72583154\t-40\n",
      "NC_047561.1\t10147466\t10147468\t-30.4647676161919\n",
      "NC_047561.1\t11783086\t11783088\t-44.1576698155646\n",
      "NC_047561.1\t16521359\t16521361\t28.8444735692442\n",
      "NC_047561.1\t19545407\t19545409\t-41.4451612903226\n",
      "NC_047561.1\t31290734\t31290736\t-30.2791262135922\n",
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\n",
      "NC_047561.1\t46808693\t46808695\t-27.2727272727273\n",
      "NC_047563.1\t11760749\t11760751\t-34.033180778032\n",
      "      28 DML-pH-25-Cov5-Gene.bed\n"
     ]
    }
   ],
   "source": [
    "#Find overlaps between DML and feature\n",
    "#Look at output\n",
    "#Count number of overlaps\n",
    "\n",
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_gene.gff \\\n",
    "> DML-pH-25-Cov5-Gene.bed\n",
    "!head DML-pH-25-Cov5-Gene.bed\n",
    "!wc -l DML-pH-25-Cov5-Gene.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t5294172\t5294174\t40.2560083594566\tNC_047559.1\tGnomon\tgene\t5232741\t5314657\t.\t+\t.\tID=gene-LOC105323223;Dbxref=GeneID:105323223;Name=LOC105323223;gbkey=Gene;gene=LOC105323223;gene_biotype=protein_coding\r\n",
      "NC_047560.1\t72583152\t72583154\t-40\tNC_047560.1\tGnomon\tgene\t72526541\t72603486\t.\t-\t.\tID=gene-LOC105330929;Dbxref=GeneID:105330929;Name=LOC105330929;gbkey=Gene;gene=LOC105330929;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t10147466\t10147468\t-30.4647676161919\tNC_047561.1\tGnomon\tgene\t10126075\t10148544\t.\t+\t.\tID=gene-LOC105337008;Dbxref=GeneID:105337008;Name=LOC105337008;gbkey=Gene;gene=LOC105337008;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t11783086\t11783088\t-44.1576698155646\tNC_047561.1\tGnomon\tgene\t11750567\t11834596\t.\t-\t.\tID=gene-LOC105346952;Dbxref=GeneID:105346952;Name=LOC105346952;gbkey=Gene;gene=LOC105346952;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t16521359\t16521361\t28.8444735692442\tNC_047561.1\tGnomon\tgene\t16519780\t16543976\t.\t-\t.\tID=gene-LOC105345244;Dbxref=GeneID:105345244;Name=LOC105345244;gbkey=Gene;gene=LOC105345244;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t19545407\t19545409\t-41.4451612903226\tNC_047561.1\tGnomon\tgene\t19544914\t19552612\t.\t-\t.\tID=gene-LOC105335660;Dbxref=GeneID:105335660;Name=LOC105335660;gbkey=Gene;gene=LOC105335660;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t31290734\t31290736\t-30.2791262135922\tNC_047561.1\tGnomon\tgene\t31288648\t31293566\t.\t+\t.\tID=gene-LOC105346771;Dbxref=GeneID:105346771;Name=LOC105346771;gbkey=Gene;gene=LOC105346771;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\tNC_047561.1\tGnomon\tgene\t40358245\t40364606\t.\t+\t.\tID=gene-LOC105324542;Dbxref=GeneID:105324542;Name=LOC105324542;gbkey=Gene;gene=LOC105324542;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t46808693\t46808695\t-27.2727272727273\tNC_047561.1\tGnomon\tgene\t46808330\t46820255\t.\t+\t.\tID=gene-LOC105321186;Dbxref=GeneID:105321186;Name=LOC105321186;gbkey=Gene;gene=LOC105321186;gene_biotype=protein_coding\r\n",
      "NC_047563.1\t11760749\t11760751\t-34.033180778032\tNC_047563.1\tGnomon\tgene\t11760153\t11763209\t.\t+\t.\tID=gene-LOC105334771;Dbxref=GeneID:105334771;Name=LOC105334771;gbkey=Gene;gene=LOC105334771;gene_biotype=protein_coding\r\n"
     ]
    }
   ],
   "source": [
    "#Find overlaps between DML and genes\n",
    "#Include original entry from gene GFF for each overlap, which will be used in downstream enrichment analyses (wb)\n",
    "#Look at output. Do not count overlaps because there are likely redundant entries\n",
    "\n",
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-wb \\\n",
    "-a DML-pH-25-Cov5-NO-SNPS.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_gene.gff \\\n",
    "> DML-pH-25-Cov5-Gene-wb.bed\n",
    "!head DML-pH-25-Cov5-Gene-wb.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      29\r\n"
     ]
    }
   ],
   "source": [
    "#Isolate column with gene IDs\n",
    "#Translate  ; and = to tabs\n",
    "#Isolate column with gene IDs\n",
    "#Sort and identify unique gene IDs\n",
    "#Count the number of unique gene IDs that contain DML\n",
    "\n",
    "!cut -f13 DML-pH-25-Cov5-Gene-wb.bed \\\n",
    "| tr \";\" \"\\t\" \\\n",
    "| tr \"=\" \"\\t\" \\\n",
    "| cut -f6 \\\n",
    "| sort | uniq \\\n",
    "| wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOC105323223\r\n",
      "LOC105330929\r\n",
      "LOC105337008\r\n",
      "LOC105346952\r\n",
      "LOC105345244\r\n",
      "LOC105335660\r\n",
      "LOC105346771\r\n",
      "LOC105324542\r\n",
      "LOC105321186\r\n",
      "LOC105334771\r\n"
     ]
    }
   ],
   "source": [
    "#Isolate gene ID information and save\n",
    "\n",
    "!cut -f13 DML-pH-25-Cov5-Gene-wb.bed \\\n",
    "| tr \";\" \"\\t\" \\\n",
    "| tr \"=\" \"\\t\" \\\n",
    "| cut -f6 \\\n",
    "> geneID-pH-DML-overlap.tab\n",
    "!head geneID-pH-DML-overlap.tab"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### ploidy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t12799610\t12799612\t27.7297297297297\n",
      "NC_047561.1\t9365798\t9365800\t34.0129358830146\n",
      "NC_047561.1\t40362698\t40362700\t29.4117647058824\n",
      "NC_047563.1\t39926052\t39926054\t42.6872058194266\n",
      "NC_047564.1\t23049738\t23049740\t29.2845880961766\n",
      "NC_047564.1\t24426622\t24426624\t-30.0865800865801\n",
      "NC_047564.1\t25380708\t25380710\t-40.1414677276746\n",
      "NC_047565.1\t10523508\t10523510\t38.0689469431726\n",
      "NC_047565.1\t13203393\t13203395\t41.1725955204216\n",
      "NC_047565.1\t14899959\t14899961\t32.5955265610438\n",
      "      20 DML-ploidy-25-Cov5-Gene.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_gene.gff \\\n",
    "> DML-ploidy-25-Cov5-Gene.bed\n",
    "!head DML-ploidy-25-Cov5-Gene.bed\n",
    "!wc -l DML-ploidy-25-Cov5-Gene.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t12799610\t12799612\t27.7297297297297\tNC_047559.1\tGnomon\tgene\t12794201\t12802669\t.\t-\t.\tID=gene-LOC105348590;Dbxref=GeneID:105348590;Name=LOC105348590;gbkey=Gene;gene=LOC105348590;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t9365798\t9365800\t34.0129358830146\tNC_047561.1\tGnomon\tgene\t9361078\t9371161\t.\t+\t.\tID=gene-LOC105331136;Dbxref=GeneID:105331136;Name=LOC105331136;gbkey=Gene;gene=LOC105331136;gene_biotype=protein_coding\r\n",
      "NC_047561.1\t40362698\t40362700\t29.4117647058824\tNC_047561.1\tGnomon\tgene\t40358245\t40364606\t.\t+\t.\tID=gene-LOC105324542;Dbxref=GeneID:105324542;Name=LOC105324542;gbkey=Gene;gene=LOC105324542;gene_biotype=protein_coding\r\n",
      "NC_047563.1\t39926052\t39926054\t42.6872058194266\tNC_047563.1\tGnomon\tgene\t39899519\t39927142\t.\t-\t.\tID=gene-LOC105326839;Dbxref=GeneID:105326839;Name=LOC105326839;gbkey=Gene;gene=LOC105326839;gene_biotype=protein_coding\r\n",
      "NC_047564.1\t23049738\t23049740\t29.2845880961766\tNC_047564.1\tGnomon\tgene\t23026724\t23059519\t.\t+\t.\tID=gene-LOC105337762;Dbxref=GeneID:105337762;Name=LOC105337762;gbkey=Gene;gene=LOC105337762;gene_biotype=protein_coding\r\n",
      "NC_047564.1\t24426622\t24426624\t-30.0865800865801\tNC_047564.1\tGnomon\tgene\t24422805\t24429598\t.\t-\t.\tID=gene-LOC105328665;Dbxref=GeneID:105328665;Name=LOC105328665;gbkey=Gene;gene=LOC105328665;gene_biotype=protein_coding\r\n",
      "NC_047564.1\t25380708\t25380710\t-40.1414677276746\tNC_047564.1\tGnomon\tgene\t25378564\t25382046\t.\t+\t.\tID=gene-LOC105317478;Dbxref=GeneID:105317478;Name=LOC105317478;gbkey=Gene;gene=LOC105317478;gene_biotype=protein_coding\r\n",
      "NC_047565.1\t10523508\t10523510\t38.0689469431726\tNC_047565.1\tGnomon\tgene\t10468342\t10543074\t.\t+\t.\tID=gene-LOC105320306;Dbxref=GeneID:105320306;Name=LOC105320306;gbkey=Gene;gene=LOC105320306;gene_biotype=protein_coding\r\n",
      "NC_047565.1\t13203393\t13203395\t41.1725955204216\tNC_047565.1\tGnomon\tgene\t13119330\t13220090\t.\t+\t.\tID=gene-LOC105329024;Dbxref=GeneID:105329024;Name=LOC105329024;gbkey=Gene;gene=LOC105329024;gene_biotype=protein_coding\r\n",
      "NC_047565.1\t14899959\t14899961\t32.5955265610438\tNC_047565.1\tGnomon\tgene\t14899770\t14913252\t.\t-\t.\tID=gene-LOC117681859;Dbxref=GeneID:117681859;Name=LOC117681859;gbkey=Gene;gene=LOC117681859;gene_biotype=protein_coding\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-wb \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_gene.gff \\\n",
    "> DML-ploidy-25-Cov5-Gene-wb.bed\n",
    "!head DML-ploidy-25-Cov5-Gene-wb.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      20\r\n"
     ]
    }
   ],
   "source": [
    "#Isolate column with gene IDs\n",
    "#Translate  ; and = to tabs\n",
    "#Isolate column with gene IDs\n",
    "#Sort and identify unique gene IDs\n",
    "#Count the number of unique gene IDs that contain DML\n",
    "\n",
    "!cut -f13 DML-ploidy-25-Cov5-Gene-wb.bed \\\n",
    "| tr \";\" \"\\t\" \\\n",
    "| tr \"=\" \"\\t\" \\\n",
    "| cut -f6 \\\n",
    "| sort | uniq \\\n",
    "| wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOC105348590\r\n",
      "LOC105331136\r\n",
      "LOC105324542\r\n",
      "LOC105326839\r\n",
      "LOC105337762\r\n",
      "LOC105328665\r\n",
      "LOC105317478\r\n",
      "LOC105320306\r\n",
      "LOC105329024\r\n",
      "LOC117681859\r\n"
     ]
    }
   ],
   "source": [
    "#Isolate gene ID information and save\n",
    "\n",
    "!cut -f13 DML-ploidy-25-Cov5-Gene-wb.bed \\\n",
    "| tr \";\" \"\\t\" \\\n",
    "| tr \"=\" \"\\t\" \\\n",
    "| cut -f6 \\\n",
    "> geneID-ploidy-DML-overlap.tab\n",
    "!head geneID-ploidy-DML-overlap.tab"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### common"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\n",
      "       1 DML-Cov5-Overlaps-Gene.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_gene.gff \\\n",
    "> DML-Cov5-Overlaps-Gene.bed\n",
    "!head DML-Cov5-Overlaps-Gene.bed\n",
    "!wc -l DML-Cov5-Overlaps-Gene.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\tNC_047561.1\tGnomon\tgene\t40358245\t40364606\t.\t+\t.\tID=gene-LOC105324542;Dbxref=GeneID:105324542;Name=LOC105324542;gbkey=Gene;gene=LOC105324542;gene_biotype=protein_coding\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-wb \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_gene.gff \\\n",
    "> DML-Cov5-Overlaps-Gene-wb.bed\n",
    "!head DML-Cov5-Overlaps-Gene-wb.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       1\r\n"
     ]
    }
   ],
   "source": [
    "#Isolate column with gene IDs\n",
    "#Translate  ; and = to tabs\n",
    "#Isolate column with gene IDs\n",
    "#Sort and identify unique gene IDs\n",
    "#Count the number of unique gene IDs that contain DML\n",
    "\n",
    "!cut -f13 DML-Cov5-Overlaps-Gene-wb.bed \\\n",
    "| tr \";\" \"\\t\" \\\n",
    "| tr \"=\" \"\\t\" \\\n",
    "| cut -f6 \\\n",
    "| sort | uniq \\\n",
    "| wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOC105324542\r\n"
     ]
    }
   ],
   "source": [
    "#Isolate gene ID information and save\n",
    "\n",
    "!cut -f13 DML-Cov5-Overlaps-Gene-wb.bed \\\n",
    "| tr \";\" \"\\t\" \\\n",
    "| tr \"=\" \"\\t\" \\\n",
    "| cut -f6 \\\n",
    "> geneID-Cov5-Overlaps-DML-overlap.tab\n",
    "!head geneID-Cov5-Overlaps-DML-overlap.tab"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4b. Exon UTR"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t10147466\t10147468\t-30.4647676161919\n",
      "NC_047563.1\t11760749\t11760751\t-34.033180778032\n",
      "NC_047564.1\t43801732\t43801734\t-26.7326732673267\n",
      "NC_047565.1\t4762558\t4762560\t-26.7316669176329\n",
      "NC_047566.1\t9548317\t9548319\t-34.3623481781376\n",
      "       5 DML-pH-25-Cov5-exonUTR.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_exonUTR.gff \\\n",
    "> DML-pH-25-Cov5-exonUTR.bed\n",
    "!head DML-pH-25-Cov5-exonUTR.bed\n",
    "!wc -l DML-pH-25-Cov5-exonUTR.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-ploidy-25-Cov5-exonUTR.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_exonUTR.gff \\\n",
    "> DML-ploidy-25-Cov5-exonUTR.bed\n",
    "!head DML-ploidy-25-Cov5-exonUTR.bed\n",
    "!wc -l DML-ploidy-25-Cov5-exonUTR.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-exonUTR.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_exonUTR.gff \\\n",
    "> DML-Cov5-Overlaps-exonUTR.bed\n",
    "!head DML-Cov5-Overlaps-exonUTR.bed\n",
    "!wc -l DML-Cov5-Overlaps-exonUTR.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4c. CDS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t11783086\t11783088\t-44.1576698155646\n",
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\n",
      "NC_047567.1\t22295946\t22295948\t-26.9118276501641\n",
      "       3 DML-pH-25-Cov5-CDS.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_CDS.gff \\\n",
    "> DML-pH-25-Cov5-CDS.bed\n",
    "!head DML-pH-25-Cov5-CDS.bed\n",
    "!wc -l DML-pH-25-Cov5-CDS.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t12799610\t12799612\t27.7297297297297\n",
      "NC_047561.1\t40362698\t40362700\t29.4117647058824\n",
      "NC_047564.1\t23049738\t23049740\t29.2845880961766\n",
      "NC_047564.1\t24426622\t24426624\t-30.0865800865801\n",
      "NC_047566.1\t46447078\t46447080\t37.3155447746109\n",
      "       5 DML-ploidy-25-Cov5-CDS.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_CDS.gff \\\n",
    "> DML-ploidy-25-Cov5-CDS.bed\n",
    "!head DML-ploidy-25-Cov5-CDS.bed\n",
    "!wc -l DML-ploidy-25-Cov5-CDS.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t40362698\t40362700\t-31.0344827586207\n",
      "       1 DML-Cov5-Overlaps-CDS.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_CDS.gff \\\n",
    "> DML-Cov5-Overlaps-CDS.bed\n",
    "!head DML-Cov5-Overlaps-CDS.bed\n",
    "!wc -l DML-Cov5-Overlaps-CDS.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4d. Intron"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t5294172\t5294174\t40.2560083594566\n",
      "NC_047560.1\t72583152\t72583154\t-40\n",
      "NC_047561.1\t16521359\t16521361\t28.8444735692442\n",
      "NC_047561.1\t19545407\t19545409\t-41.4451612903226\n",
      "NC_047561.1\t31290734\t31290736\t-30.2791262135922\n",
      "NC_047561.1\t46808693\t46808695\t-27.2727272727273\n",
      "NC_047563.1\t66794619\t66794621\t-29.651103651714\n",
      "NC_047564.1\t2678443\t2678445\t-45.6953642384106\n",
      "NC_047565.1\t10619872\t10619874\t-25.6880733944954\n",
      "NC_047565.1\t24575356\t24575358\t-28.0575539568345\n",
      "      20 DML-pH-25-Cov5-intron.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_intron.bed \\\n",
    "> DML-pH-25-Cov5-intron.bed\n",
    "!head DML-pH-25-Cov5-intron.bed\n",
    "!wc -l DML-pH-25-Cov5-intron.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t9365798\t9365800\t34.0129358830146\n",
      "NC_047563.1\t39926052\t39926054\t42.6872058194266\n",
      "NC_047564.1\t25380708\t25380710\t-40.1414677276746\n",
      "NC_047565.1\t10523508\t10523510\t38.0689469431726\n",
      "NC_047565.1\t13203393\t13203395\t41.1725955204216\n",
      "NC_047565.1\t14899959\t14899961\t32.5955265610438\n",
      "NC_047566.1\t27129225\t27129227\t37.7269975786925\n",
      "NC_047566.1\t35988011\t35988013\t-53.0531425651507\n",
      "NC_047566.1\t46084094\t46084096\t-32.3234916559692\n",
      "NC_047566.1\t50117081\t50117083\t32.0492517222266\n",
      "      15 DML-ploidy-25-Cov5-intron.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_intron.bed \\\n",
    "> DML-ploidy-25-Cov5-intron.bed\n",
    "!head DML-ploidy-25-Cov5-intron.bed\n",
    "!wc -l DML-ploidy-25-Cov5-intron.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-intron.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_intron.bed \\\n",
    "> DML-Cov5-Overlaps-intron.bed\n",
    "!head DML-Cov5-Overlaps-intron.bed\n",
    "!wc -l DML-Cov5-Overlaps-intron.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4e. Upstream flanks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-pH-25-Cov5-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_upstream.gff \\\n",
    "> DML-pH-25-Cov5-upstream.bed\n",
    "!head DML-pH-25-Cov5-upstream.bed\n",
    "!wc -l DML-pH-25-Cov5-upstream.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-ploidy-25-Cov5-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_upstream.gff \\\n",
    "> DML-ploidy-25-Cov5-upstream.bed\n",
    "!head DML-ploidy-25-Cov5-upstream.bed\n",
    "!wc -l DML-ploidy-25-Cov5-upstream.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_upstream.gff \\\n",
    "> DML-Cov5-Overlaps-upstream.bed\n",
    "!head DML-Cov5-Overlaps-upstream.bed\n",
    "!wc -l DML-Cov5-Overlaps-upstream.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4f. Downstream flanks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047561.1\t19286180\t19286182\t-55.4137931034483\n",
      "NC_047561.1\t21915577\t21915579\t46.9271523178808\n",
      "NC_047567.1\t16984837\t16984839\t42.8241335044929\n",
      "NW_022994991.1\t19672\t19674\t36.769801980198\n",
      "       4 DML-pH-25-Cov5-downstream.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_downstream.gff \\\n",
    "> DML-pH-25-Cov5-downstream.bed\n",
    "!head DML-pH-25-Cov5-downstream.bed\n",
    "!wc -l DML-pH-25-Cov5-downstream.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047566.1\t24265305\t24265307\t-26.1261261261261\n",
      "       1 DML-ploidy-25-Cov5-downstream.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_downstream.gff \\\n",
    "> DML-ploidy-25-Cov5-downstream.bed\n",
    "!head DML-ploidy-25-Cov5-downstream.bed\n",
    "!wc -l DML-ploidy-25-Cov5-downstream.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-downstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_downstream.gff \\\n",
    "> DML-Cov5-Overlaps-downstream.bed\n",
    "!head DML-Cov5-Overlaps-downstream.bed\n",
    "!wc -l DML-Cov5-Overlaps-downstream.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4g. Intergenic regions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047560.1\t66080783\t66080785\t-51.6483516483517\n",
      "NC_047565.1\t44521815\t44521817\t-30.3333333333333\n",
      "       2 DML-pH-25-Cov5-intergenic.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_intergenic.bed \\\n",
    "> DML-pH-25-Cov5-intergenic.bed\n",
    "!head DML-pH-25-Cov5-intergenic.bed\n",
    "!wc -l DML-pH-25-Cov5-intergenic.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t53732861\t53732863\t25.8426966292135\n",
      "NC_047566.1\t24266096\t24266098\t-29.4736842105263\n",
      "NC_047566.1\t24266109\t24266111\t-27.7777777777778\n",
      "       3 DML-ploidy-25-Cov5-intergenic.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_intergenic.bed \\\n",
    "> DML-ploidy-25-Cov5-intergenic.bed\n",
    "!head DML-ploidy-25-Cov5-intergenic.bed\n",
    "!wc -l DML-ploidy-25-Cov5-intergenic.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-intergenic.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_intergenic.bed \\\n",
    "> DML-Cov5-Overlaps-intergenic.bed\n",
    "!head DML-Cov5-Overlaps-intergenic.bed\n",
    "!wc -l DML-Cov5-Overlaps-intergenic.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4h. lncRNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047564.1\t43801732\t43801734\t-26.7326732673267\n",
      "NC_047565.1\t44578741\t44578743\t-26.7896446913321\n",
      "NC_047566.1\t9548317\t9548319\t-34.3623481781376\n",
      "       3 DML-pH-25-Cov5-lncRNA.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_lncRNA.gff \\\n",
    "> DML-pH-25-Cov5-lncRNA.bed\n",
    "!head DML-pH-25-Cov5-lncRNA.bed\n",
    "!wc -l DML-pH-25-Cov5-lncRNA.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-ploidy-25-Cov5-lncRNA.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_lncRNA.gff \\\n",
    "> DML-ploidy-25-Cov5-lncRNA.bed\n",
    "!head DML-ploidy-25-Cov5-lncRNA.bed\n",
    "!wc -l DML-ploidy-25-Cov5-lncRNA.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-lncRNA.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_lncRNA.gff \\\n",
    "> DML-Cov5-Overlaps-lncRNA.bed\n",
    "!head DML-Cov5-Overlaps-lncRNA.bed\n",
    "!wc -l DML-Cov5-Overlaps-lncRNA.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4i. Tranposable elements"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t5294172\t5294174\t40.2560083594566\n",
      "NC_047560.1\t66080783\t66080785\t-51.6483516483517\n",
      "NC_047561.1\t19286180\t19286182\t-55.4137931034483\n",
      "NC_047561.1\t21915577\t21915579\t46.9271523178808\n",
      "NC_047564.1\t2678443\t2678445\t-45.6953642384106\n",
      "NC_047565.1\t10619872\t10619874\t-25.6880733944954\n",
      "NC_047565.1\t44521815\t44521817\t-30.3333333333333\n",
      "NC_047565.1\t44578741\t44578743\t-26.7896446913321\n",
      "NC_047566.1\t23226898\t23226900\t25.3731343283582\n",
      "NC_047567.1\t16984837\t16984839\t42.8241335044929\n",
      "      15 DML-pH-25-Cov5-TE.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-pH-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_rm.te.bed \\\n",
    "> DML-pH-25-Cov5-TE.bed\n",
    "!head DML-pH-25-Cov5-TE.bed\n",
    "!wc -l DML-pH-25-Cov5-TE.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NC_047559.1\t53732861\t53732863\t25.8426966292135\n",
      "NC_047561.1\t9365798\t9365800\t34.0129358830146\n",
      "NC_047563.1\t39926052\t39926054\t42.6872058194266\n",
      "NC_047566.1\t50117081\t50117083\t32.0492517222266\n",
      "NC_047566.1\t51204319\t51204321\t35.812086064308\n",
      "NC_047567.1\t21017447\t21017449\t34.8875423641779\n",
      "       6 DML-ploidy-25-Cov5-TE.bed\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-ploidy-25-Cov5-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_rm.te.bed \\\n",
    "> DML-ploidy-25-Cov5-TE.bed\n",
    "!head DML-ploidy-25-Cov5-TE.bed\n",
    "!wc -l DML-ploidy-25-Cov5-TE.bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       0 DML-Cov5-Overlaps-TE.bed\r\n"
     ]
    }
   ],
   "source": [
    "!{bedtoolsDirectory}intersectBed \\\n",
    "-u \\\n",
    "-a DML-Cov5-Overlaps-NO-SNPs.bed \\\n",
    "-b ../../genome-feature-files/cgigas_uk_roslin_v1_rm.te.bed \\\n",
    "> DML-Cov5-Overlaps-TE.bed\n",
    "!head DML-Cov5-Overlaps-TE.bed\n",
    "!wc -l DML-Cov5-Overlaps-TE.bed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## 5. Obtain line counts for overlap files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This will help with downstream visualization."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 6a. pH-DML"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DML-pH-25-Cov5-CDS.bed\r\n",
      "DML-pH-25-Cov5-Gene-wb.bed\r\n",
      "DML-pH-25-Cov5-Gene.bed\r\n",
      "DML-pH-25-Cov5-NO-SNPs.bed\r\n",
      "DML-pH-25-Cov5-TE.bed\r\n",
      "DML-pH-25-Cov5-downstream.bed\r\n",
      "DML-pH-25-Cov5-exonUTR.bed\r\n",
      "DML-pH-25-Cov5-intergenic.bed\r\n",
      "DML-pH-25-Cov5-intron.bed\r\n",
      "DML-pH-25-Cov5-lncRNA.bed\r\n",
      "DML-pH-25-Cov5-unique-CT-SNPs.bed\r\n",
      "DML-pH-25-Cov5-upstream.bed\r\n",
      "DML-pH-25-Cov5.csv.bed\r\n"
     ]
    }
   ],
   "source": [
    "!find DML-pH-25-*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Get line count for all DML overlap files\n",
    "#Remove the 13th line (total entries)\n",
    "#Remove 11th line (unique SNP overlaps)\n",
    "#Remove 4th line (true DML list)\n",
    "#Print in a tab-delimited format\n",
    "#Save output\n",
    "\n",
    "!wc -l DML-pH-25-* \\\n",
    "| sed '13,$ d' \\\n",
    "| sed '11d' \\\n",
    "| sed '4d' \\\n",
    "| awk '{print $1\"\\t\"$2}' \\\n",
    "> DML-pH-25-Overlap-counts.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3\tDML-pH-25-Cov5-CDS.bed\r\n",
      "31\tDML-pH-25-Cov5-Gene-wb.bed\r\n",
      "28\tDML-pH-25-Cov5-Gene.bed\r\n",
      "15\tDML-pH-25-Cov5-TE.bed\r\n",
      "4\tDML-pH-25-Cov5-downstream.bed\r\n",
      "5\tDML-pH-25-Cov5-exonUTR.bed\r\n",
      "2\tDML-pH-25-Cov5-intergenic.bed\r\n",
      "20\tDML-pH-25-Cov5-intron.bed\r\n",
      "3\tDML-pH-25-Cov5-lncRNA.bed\r\n",
      "0\tDML-pH-25-Cov5-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!cat DML-pH-25-Overlap-counts.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 6b. ploidy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DML-ploidy-25-Cov5-CDS.bed\r\n",
      "DML-ploidy-25-Cov5-Gene-wb.bed\r\n",
      "DML-ploidy-25-Cov5-Gene.bed\r\n",
      "DML-ploidy-25-Cov5-NO-SNPs.bed\r\n",
      "DML-ploidy-25-Cov5-TE.bed\r\n",
      "DML-ploidy-25-Cov5-downstream.bed\r\n",
      "DML-ploidy-25-Cov5-exonUTR.bed\r\n",
      "DML-ploidy-25-Cov5-intergenic.bed\r\n",
      "DML-ploidy-25-Cov5-intron.bed\r\n",
      "DML-ploidy-25-Cov5-lncRNA.bed\r\n",
      "DML-ploidy-25-Cov5-unique-CT-SNPs.bed\r\n",
      "DML-ploidy-25-Cov5-upstream.bed\r\n",
      "DML-ploidy-25-Cov5.csv.bed\r\n"
     ]
    }
   ],
   "source": [
    "!find DML-ploidy-25-*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 93,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Get line count for all DML overlap files\n",
    "#Remove the 13th line (total entries)\n",
    "#Remove 11th line (unique SNP overlaps)\n",
    "#Remove 4th line (true DML list)\n",
    "#Print in a tab-delimited format\n",
    "#Save output\n",
    "\n",
    "!wc -l DML-ploidy-25-* \\\n",
    "| sed '13,$ d' \\\n",
    "| sed '11d' \\\n",
    "| sed '4d' \\\n",
    "| awk '{print $1\"\\t\"$2}' \\\n",
    "> DML-ploidy-25-Overlap-counts.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "5\tDML-ploidy-25-Cov5-CDS.bed\r\n",
      "20\tDML-ploidy-25-Cov5-Gene-wb.bed\r\n",
      "20\tDML-ploidy-25-Cov5-Gene.bed\r\n",
      "6\tDML-ploidy-25-Cov5-TE.bed\r\n",
      "1\tDML-ploidy-25-Cov5-downstream.bed\r\n",
      "0\tDML-ploidy-25-Cov5-exonUTR.bed\r\n",
      "3\tDML-ploidy-25-Cov5-intergenic.bed\r\n",
      "15\tDML-ploidy-25-Cov5-intron.bed\r\n",
      "0\tDML-ploidy-25-Cov5-lncRNA.bed\r\n",
      "0\tDML-ploidy-25-Cov5-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!cat DML-ploidy-25-Overlap-counts.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 6c. common"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DML-Cov5-Overlaps-CDS.bed\r\n",
      "DML-Cov5-Overlaps-Gene-wb.bed\r\n",
      "DML-Cov5-Overlaps-Gene.bed\r\n",
      "DML-Cov5-Overlaps-NO-SNPs.bed\r\n",
      "DML-Cov5-Overlaps-TE.bed\r\n",
      "DML-Cov5-Overlaps-downstream.bed\r\n",
      "DML-Cov5-Overlaps-exonUTR.bed\r\n",
      "DML-Cov5-Overlaps-intergenic.bed\r\n",
      "DML-Cov5-Overlaps-intron.bed\r\n",
      "DML-Cov5-Overlaps-lncRNA.bed\r\n",
      "DML-Cov5-Overlaps-unique-CT-SNPs.bed\r\n",
      "DML-Cov5-Overlaps-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!find DML-Cov5-Overlaps-*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Get line count for all DML overlap files\n",
    "#Remove the 13th line (total entries)\n",
    "#Remove 12th line (unique SNP overlaps)\n",
    "#Remove 4th line (true DML list)\n",
    "#Print in a tab-delimited format\n",
    "#Save output\n",
    "\n",
    "!wc -l DML-Cov5-Overlaps-* \\\n",
    "| sed '14,$ d' \\\n",
    "| sed '12d' \\\n",
    "| sed '4d' \\\n",
    "| awk '{print $1\"\\t\"$2}' \\\n",
    "> DML-Cov5-Overlaps-counts.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 115,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1\tDML-Cov5-Overlaps-CDS.bed\r\n",
      "1\tDML-Cov5-Overlaps-Gene-wb.bed\r\n",
      "1\tDML-Cov5-Overlaps-Gene.bed\r\n",
      "0\tDML-Cov5-Overlaps-TE.bed\r\n",
      "0\tDML-Cov5-Overlaps-counts.txt\r\n",
      "0\tDML-Cov5-Overlaps-downstream.bed\r\n",
      "0\tDML-Cov5-Overlaps-exonUTR.bed\r\n",
      "0\tDML-Cov5-Overlaps-intergenic.bed\r\n",
      "0\tDML-Cov5-Overlaps-intron.bed\r\n",
      "0\tDML-Cov5-Overlaps-lncRNA.bed\r\n",
      "0\tDML-Cov5-Overlaps-upstream.bed\r\n"
     ]
    }
   ],
   "source": [
    "!cat DML-Cov5-Overlaps-counts.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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