<commit_before>{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4A4D.png\" alt=\"Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4A4D.png\" width=50%/>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "bsmaploc=\"/Users/Shared/Apps/bsmap-2.74/\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Volumes/web-1/halfshell/working-directory/16-10-17\n"
     ]
    }
   ],
   "source": [
    "cd /Volumes/web-1/halfshell/working-directory/16-10-17"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "  1  502M    1 9130k    0     0  89608      0  1:38:00  0:01:44  1:36:16 90660\n",
      "curl: (18) transfer closed with 517615836 bytes remaining to read\n",
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "  2  637M    2 14.0M    0     0   244k      0  0:44:35  0:00:58  0:43:37  312k"
     ]
    }
   ],
   "source": [
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/1_ATCACG_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/2_CGATGT_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/3_TTAGGC_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/5_ACAGTG_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/6_GCCAAT_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/7_CAGATC_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/8_ACTTGA_L001_R1_001.fastq.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4D68.png\" alt=\"Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4D68.png\"/>\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Genome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Volumes/caviar/wd/data\n"
     ]
    }
   ],
   "source": [
    "cd ../data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!curl -O http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {<commit_msg>Restart genefish bs<commit_after>{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4A4D.png\" alt=\"Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4A4D.png\" width=50%/>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "bsmaploc=\"/Users/Shared/Apps/bsmap-2.74/\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Volumes/web/halfshell/working-directory/16-10-17\n"
     ]
    }
   ],
   "source": [
    "cd /Volumes/web/halfshell/working-directory/16-10-17"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 5392464\r\n",
      "-rw-rw-rw-  1 Steven  staff   8.9M Oct 17 12:06 1_ATCACG_L001_R1_001.fastq.gz\r\n",
      "-rw-rw-rw-  1 Steven  staff   638M Oct 17 12:14 2_CGATGT_L001_R1_001.fastq.gz\r\n",
      "-rw-rw-rw-  1 Steven  staff   633M Oct 17 12:20 3_TTAGGC_L001_R1_001.fastq.gz\r\n",
      "-rw-rw-rw-  1 Steven  staff   671M Oct 17 12:25 5_ACAGTG_L001_R1_001.fastq.gz\r\n",
      "-rw-rw-rw-  1 Steven  staff   667M Oct 17 12:29 6_GCCAAT_L001_R1_001.fastq.gz\r\n",
      "-rw-rw-rw-  1 Steven  staff    15M Oct 17 12:29 7_CAGATC_L001_R1_001.fastq.gz\r\n"
     ]
    }
   ],
   "source": [
    "!ls -lh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100  548M  100  548M    0     0  23.6M      0  0:00:23  0:00:23 --:--:-- 25.9M\n",
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100  764M  100  764M    0     0  13.2M      0  0:00:57  0:00:57 --:--:-- 17.5M\n"
     ]
    }
   ],
   "source": [
    "\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/7_CAGATC_L001_R1_001.fastq.gz\n",
    "!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/8_ACTTGA_L001_R1_001.fastq.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4D68.png\" alt=\"Whole_genome_BSseq_December_2015_·_RobertsLab_project-olympia_oyster-genomic_Wiki_1DAD4D68.png\"/>\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Genome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Volumes/caviar/wd/data\n"
     ]
    }
   ],
   "source": [
    "cd ../data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100  761M  100  761M    0     0  14.3M      0  0:00:53  0:00:53 --:--:-- 15.5M\n"
     ]
    }
   ],
   "source": [
    "!curl -O http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/Ostrea_lurida.scafSeq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
{'fraction_non_alphanumeric': 0.17115649667961408, 'fraction_numerical': 0.06026813682495928, 'mean_word_length': 2.2606209150326797, 'pattern_counts': {'":': 128, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 5, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4257996', 'n_tokens_mistral': 3653, 'n_tokens_neox': 3281, 'n_words': 463}