jupyter_nbs/sam/20160516_Oly_Small_Insert_Library_Genome_Read_Counts.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Mon May 16 08:27:10 PDT 2016\r\n"
     ]
    }
   ],
   "source": [
    "!date"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Software:\n",
      "\n",
      "    System Software Overview:\n",
      "\n",
      "      System Version: Mac OS X 10.7.5 (11G63)\n",
      "      Kernel Version: Darwin 11.4.2\n",
      "      Boot Volume: SSD2\n",
      "      Boot Mode: Normal\n",
      "      Computer Name: greenbird (2)\n",
      "      User Name: Sam (Sam)\n",
      "      Secure Virtual Memory: Enabled\n",
      "      64-bit Kernel and Extensions: No\n",
      "      Time since boot: 5 days 1:46\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "system_profiler SPSoftwareDataType"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "      Model Name: Mac Pro\n",
      "      Model Identifier: MacPro1,1\n",
      "      Processor Name: Dual-Core Intel Xeon\n",
      "      Processor Speed: 3 GHz\n",
      "      Number of Processors: 2\n",
      "      Total Number of Cores: 4\n",
      "      L2 Cache (per Processor): 4 MB\n",
      "      Memory: 14 GB\n",
      "      Bus Speed: 1.33 GHz\n",
      "      Boot ROM Version: MP11.005C.B08\n",
      "      SMC Version (system): 1.7f10\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "#Uses grep to exclude lines that display serial number and hardware UUID\n",
    "system_profiler SPHardwareDataType | grep -v [SH][ea]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### List files provided by BGI"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz.clean.dup.clean.gz\n",
      "151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz.clean.dup.clean.gz\n",
      "151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz.clean.dup.clean.gz\n",
      "151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz\n",
      "151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz\n",
      "151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz.clean.dup.clean.gz\n",
      "20160512_F15FTSUSAT0327_genome_survey.pdf\n",
      "Ostrea_lurida.GC_content_vs_depth.png\n",
      "Ostrea_lurida.scafSeq\n",
      "README\n",
      "md5.txt\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "ls /Volumes/web/O_lurida_genome_assemblies_BGI/20160512/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Create checksums file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "real\t43m39.240s\n",
      "user\t1m32.906s\n",
      "sys\t2m27.982s\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "\n",
    "#For loop generates a md5 checksum has value for each file\n",
    "#and appends the output to the checksums.md5 file.\n",
    "time for file in /Volumes/web/O_lurida_genome_assemblies_BGI/20160512/*.gz\n",
    "    do\n",
    "        md5 \"$file\" >> /Volumes/web/O_lurida_genome_assemblies_BGI/20160512/checksums.md5\n",
    "        done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Calculate total number of reads generated by this project.¶\n",
    "#### Calculate number of reads per file, append filename and corresponding number of reads to readme file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz.clean.dup.clean.gz\t61253141\n",
      "151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz.clean.dup.clean.gz\t61253141\n",
      "151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz.clean.dup.clean.gz\t58755925\n",
      "151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz\t58755925\n",
      "151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz\t43938762\n",
      "151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz.clean.dup.clean.gz\t43938762\n",
      "327895656\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "real\t59m24.186s\n",
      "user\t19m15.868s\n",
      "sys\t3m29.110s\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "\n",
    "#Initializes variable.\n",
    "totalreads=0\n",
    "\n",
    "#For loop counts the lines in each file and divides them by four. This is performed because\n",
    "#Illumina sequencing files are composed of four lines per read.\n",
    "#A running total of the total number of reads is generated [totalreads=$((readcount+totalreads))]\n",
    "#and is printed after the for loop completes.\n",
    "\n",
    "#Format the output (printf) to print the filename, followed by a tab, followed by the readcount.\n",
    "#The command \"tee -a\" is used to both print the output to the screen and append the output to the readme.md file.\n",
    "time for file in /Volumes/web/O_lurida_genome_assemblies_BGI/20160512/*.gz\n",
    "    do linecount=`gunzip -c \"$file\" | wc -l`\n",
    "    readcount=$((linecount/4))\n",
    "    totalreads=$((readcount+totalreads))\n",
    "    printf \"%s\\t%s\\n\" \"${file##*/}\" \"$readcount\" | tee -a /Volumes/web/O_lurida_genome_assemblies_BGI/20160512/readme.md\n",
    "done\n",
    "echo $totalreads"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Count the number of sequences in the scafSeq (FASTA format) file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  765755\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "real\t1m7.420s\n",
      "user\t0m0.919s\n",
      "sys\t0m2.288s\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "time grep \">\" /Volumes/web/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq | wc -l"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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