{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# The Unix Shell: File and Directory Management"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Listing files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "avg.sh\t\t\tcat_if_exists.sh\textract_headers.sh\n"
     ]
    }
   ],
   "source": [
    "ls scripts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Include hidden files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ".\n",
      "..\n",
      ".DS_Store\n",
      ".gitignore\n",
      ".ipynb_checkpoints\n",
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls -a"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Exclude current and parent directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ".DS_Store\n",
      ".gitignore\n",
      ".ipynb_checkpoints\n",
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls -A"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Show details"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 280\n",
      "-rw-r--r--  1 cliburn  staff      0 Jun  9 08:23 0\n",
      "-rw-r--r--  1 cliburn  staff   7378 May  2 17:21 01_The_Unix_Shell.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  11613 Jun  7 18:22 01_The_Unix_Shell_Solutions.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  27356 Jun  9 09:01 The Unix Shell - File and Directory Management.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  23128 Jun  8 18:25 The Unix Shell - Finding Stuff.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  18214 Jun  8 11:29 The Unix Shell - Getting Help.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  23346 Jun  9 08:50 The Unix Shell - Shell Scripts.ipynb\n",
      "-rw-r--r--  1 cliburn  staff   8386 Jun  8 14:04 The Unix Shell - Working with Text.ipynb\n",
      "drwxr-xr-x  6 cliburn  staff    204 Jun  9 08:38 data\n",
      "-rw-r--r--  1 cliburn  staff     45 Jun  8 11:58 hello.txt\n",
      "-rw-r--r--  1 cliburn  staff      0 Jun  8 12:03 one two three\n",
      "drwxr-xr-x  6 cliburn  staff    204 Jun  9 08:46 scripts\n",
      "-rw-r--r--  1 cliburn  staff     42 Jun  8 11:58 stderr.txt\n",
      "-rw-r--r--  1 cliburn  staff      0 Jun  8 11:58 stdout.txt\n",
      "-rw-r--r--  1 cliburn  staff     50 Jun  8 12:06 test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls -l"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Sort by last modified time"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 280\n",
      "-rw-r--r--  1 cliburn  staff  27356 Jun  9 09:01 The Unix Shell - File and Directory Management.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  23346 Jun  9 08:50 The Unix Shell - Shell Scripts.ipynb\n",
      "drwxr-xr-x  6 cliburn  staff    204 Jun  9 08:46 scripts\n",
      "drwxr-xr-x  6 cliburn  staff    204 Jun  9 08:38 data\n",
      "-rw-r--r--  1 cliburn  staff      0 Jun  9 08:23 0\n",
      "-rw-r--r--  1 cliburn  staff  23128 Jun  8 18:25 The Unix Shell - Finding Stuff.ipynb\n",
      "-rw-r--r--  1 cliburn  staff   8386 Jun  8 14:04 The Unix Shell - Working with Text.ipynb\n",
      "-rw-r--r--  1 cliburn  staff     50 Jun  8 12:06 test1.txt\n",
      "-rw-r--r--  1 cliburn  staff      0 Jun  8 12:03 one two three\n",
      "-rw-r--r--  1 cliburn  staff     42 Jun  8 11:58 stderr.txt\n",
      "-rw-r--r--  1 cliburn  staff      0 Jun  8 11:58 stdout.txt\n",
      "-rw-r--r--  1 cliburn  staff     45 Jun  8 11:58 hello.txt\n",
      "-rw-r--r--  1 cliburn  staff  18214 Jun  8 11:29 The Unix Shell - Getting Help.ipynb\n",
      "-rw-r--r--  1 cliburn  staff  11613 Jun  7 18:22 01_The_Unix_Shell_Solutions.ipynb\n",
      "-rw-r--r--  1 cliburn  staff   7378 May  2 17:21 01_The_Unix_Shell.ipynb\n"
     ]
    }
   ],
   "source": [
    "ls -lt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Human readable output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 280\n",
      "-rw-r--r--  1 cliburn  staff    27K Jun  9 09:01 The Unix Shell - File and Directory Management.ipynb\n",
      "-rw-r--r--  1 cliburn  staff    23K Jun  9 08:50 The Unix Shell - Shell Scripts.ipynb\n",
      "drwxr-xr-x  6 cliburn  staff   204B Jun  9 08:46 scripts\n",
      "drwxr-xr-x  6 cliburn  staff   204B Jun  9 08:38 data\n",
      "-rw-r--r--  1 cliburn  staff     0B Jun  9 08:23 0\n",
      "-rw-r--r--  1 cliburn  staff    23K Jun  8 18:25 The Unix Shell - Finding Stuff.ipynb\n",
      "-rw-r--r--  1 cliburn  staff   8.2K Jun  8 14:04 The Unix Shell - Working with Text.ipynb\n",
      "-rw-r--r--  1 cliburn  staff    50B Jun  8 12:06 test1.txt\n",
      "-rw-r--r--  1 cliburn  staff     0B Jun  8 12:03 one two three\n",
      "-rw-r--r--  1 cliburn  staff    42B Jun  8 11:58 stderr.txt\n",
      "-rw-r--r--  1 cliburn  staff     0B Jun  8 11:58 stdout.txt\n",
      "-rw-r--r--  1 cliburn  staff    45B Jun  8 11:58 hello.txt\n",
      "-rw-r--r--  1 cliburn  staff    18K Jun  8 11:29 The Unix Shell - Getting Help.ipynb\n",
      "-rw-r--r--  1 cliburn  staff    11K Jun  7 18:22 01_The_Unix_Shell_Solutions.ipynb\n",
      "-rw-r--r--  1 cliburn  staff   7.2K May  2 17:21 01_The_Unix_Shell.ipynb\n"
     ]
    }
   ],
   "source": [
    "ls -lth"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Recursive listing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n",
      "\n",
      "./data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "./scripts:\n",
      "avg.sh\t\t\tcat_if_exists.sh\textract_headers.sh\n"
     ]
    }
   ],
   "source": [
    "ls -R"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Globbing\n",
    "\n",
    "The use of wild cards to specify Unix paths is known as globbing."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### `*` represets any number of characters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n"
     ]
    }
   ],
   "source": [
    "ls *ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data/example.fna\tdata/iris.csv\t\tdata/iris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data/*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### `?` represents exactly one character"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data/iris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data/iris??.csv"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Character sets\n",
    "\n",
    "- `[abc]` represents a or b or c\n",
    "- [a-z] represents any lower case character\n",
    "- `!` negates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\t\t\t\t\t01_The_Unix_Shell_Solutions.ipynb\n",
      "01_The_Unix_Shell.ipynb\n"
     ]
    }
   ],
   "source": [
    "ls [0-9]*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "hello.txt\n",
      "one two three\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n",
      "\n",
      "data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "scripts:\n",
      "avg.sh\t\t\tcat_if_exists.sh\textract_headers.sh\n"
     ]
    }
   ],
   "source": [
    "ls [!0-9]*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Spitting paths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821-2017/lessons\n"
     ]
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821-2017\n"
     ]
    }
   ],
   "source": [
    "dirname $(pwd)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lessons\n"
     ]
    }
   ],
   "source": [
    "basename $(pwd)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821\n"
     ]
    }
   ],
   "source": [
    "pwd | xargs dirname"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lessons\n"
     ]
    }
   ],
   "source": [
    "pwd | xargs basename"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Directory navigation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Show current directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821/lessons\n"
     ]
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Move to parent directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cd .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821\n"
     ]
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Move back to last directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821/lessons\n"
     ]
    }
   ],
   "source": [
    "cd -"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Move using relative addressing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cd data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821/lessons/data\n"
     ]
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Move using absolute addressing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cd /Users/cliburn/_teach/bios-821/lessons"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/cliburn/_teach/bios-821/lessons\n"
     ]
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Making and removing new directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mkdir foo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "foo\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Making intermediate directories automatically"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mkdir -p a/b/c/d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "b\n",
      "\n",
      "a/b:\n",
      "c\n",
      "\n",
      "a/b/c:\n",
      "d\n",
      "\n",
      "a/b/c/d:\n"
     ]
    }
   ],
   "source": [
    "ls -R a"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Deleting directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rmdir foo"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Only works if directory is empty\n",
    "\n",
    "The `| cat` part is not necessary on the command line, but is only used here for convenience of Run All Cells as Jupyter stops on non-zero exit codes. The `| cat` syntax \"pipes\" the output of `rmdir data` to a the `cat` program."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "rmdir: data: Directory not empty\n"
     ]
    }
   ],
   "source": [
    "rmdir data | cat"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Recursive intermediate directories as well"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rmdir -p a/b/c/d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Working with files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Making an empty file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "touch foo.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "foo.txt\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Deleting a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm foo.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Viewing a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#!/bin/bash                                                                     \n",
      "sum=0\n",
      "n=0\n",
      "while read line\n",
      "do\n",
      "    if [ ! -z \"$line\" ]\n",
      "    then\n",
      "        n=$((n+1))\n",
      "        sum=$(echo $sum + $line | bc)\n",
      "    fi\n",
      "done\n",
      "echo $sum / $n | bc -l\n"
     ]
    }
   ],
   "source": [
    "cat scripts/avg.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#!/bin/bash                                                                     \n",
      "sum=0\n",
      "n=0\n"
     ]
    }
   ],
   "source": [
    "head -n 3 scripts/avg.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    fi\n",
      "done\n",
      "echo $sum / $n | bc -l\n"
     ]
    }
   ],
   "source": [
    "tail -n 3 scripts/avg.sh"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Can start tail form a specified line number with (+)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "while read line\n",
      "do\n",
      "    if [ ! -z \"$line\" ]\n",
      "    then\n",
      "        n=$((n+1))\n",
      "        sum=$(echo $sum + $line | bc)\n",
      "    fi\n",
      "done\n",
      "echo $sum / $n | bc -l\n"
     ]
    }
   ],
   "source": [
    "tail -n +4 scripts/avg.sh"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Copying and moving files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Copying files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cp \"The Unix Shell - File and Directory Management.ipynb\" The_Unix_Shell.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "The_Unix_Shell.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Copying directories (Recursive copy)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cp -R data data2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "The_Unix_Shell.ipynb\n",
      "data\n",
      "data2\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n",
      "\n",
      "./data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "./data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "./scripts:\n",
      "avg.sh\t\t\tcat_if_exists.sh\textract_headers.sh\n"
     ]
    }
   ],
   "source": [
    "ls -R"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Renaming a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mv The_Unix_Shell.ipynb The_Unix_Shell_Copy.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "The_Unix_Shell_Copy.ipynb\n",
      "data\n",
      "data2\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Move a file to a new location"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mv The_Unix_Shell_Copy.ipynb scripts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "data2\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n",
      "\n",
      "./data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "./data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "./scripts:\n",
      "The_Unix_Shell_Copy.ipynb\tcat_if_exists.sh\n",
      "avg.sh\t\t\t\textract_headers.sh\n"
     ]
    }
   ],
   "source": [
    "ls -R"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## File compression and archival"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Combine multiple files into single file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "BSDTAR(1)                 BSD General Commands Manual                BSDTAR(1)\n",
      "\n",
      "NAME\n",
      "     tar -- manipulate tape archives\n",
      "\n",
      "SYNOPSIS\n",
      "     tar [bundled-flags <args>] [<file> | <pattern> ...]\n",
      "     tar {-c} [options] [files | directories]\n",
      "     tar {-r | -u} -f archive-file [options] [files | directories]\n",
      "     tar {-t | -x} [options] [patterns]\n",
      "\n",
      "DESCRIPTION\n",
      "     tar creates and manipulates streaming archive files.  This implementation\n",
      "     can extract from tar, pax, cpio, zip, jar, ar, and ISO 9660 cdrom images\n",
      "     and can create tar, pax, cpio, ar, and shar archives.\n",
      "\n",
      "     The first synopsis form shows a ``bundled'' option word.  This usage is\n",
      "     provided for compatibility with historical implementations.  See COMPATI-\n",
      "     BILITY below for details.\n"
     ]
    }
   ],
   "source": [
    "man tar | head -n 20"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "a data\n",
      "a data/.ipynb_checkpoints\n",
      "a data/example.fna\n",
      "a data/iris.csv\n",
      "a data/iris24.csv\n"
     ]
    }
   ],
   "source": [
    "tar -cvf data.tar data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm -rf data/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data.tar\n",
      "\n",
      "data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Compress concatenated file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "gzip data.tar"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data.tar.gz\n",
      "\n",
      "data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Uncompress"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "gunzip data.tar.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data.tar\n",
      "\n",
      "data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Recover original files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "x data/\n",
      "x data/.ipynb_checkpoints/\n",
      "x data/example.fna\n",
      "x data/iris.csv\n",
      "x data/iris24.csv\n"
     ]
    }
   ],
   "source": [
    "tar -xvf data.tar"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data.tar\n",
      "\n",
      "data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm data.tar"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Concatenate and compress"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "a data\n",
      "a data/.ipynb_checkpoints\n",
      "a data/example.fna\n",
      "a data/iris.csv\n",
      "a data/iris24.csv\n"
     ]
    }
   ],
   "source": [
    "tar -cvzf data.tar.gz data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm -rf data/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data.tar.gz\n",
      "\n",
      "data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Uncompress and recover"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "x data/\n",
      "x data/.ipynb_checkpoints/\n",
      "x data/example.fna\n",
      "x data/iris.csv\n",
      "x data/iris24.csv\n"
     ]
    }
   ],
   "source": [
    "tar -xvzf data.tar.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data.tar.gz\n",
      "\n",
      "data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "data2:\n",
      "example.fna\tiris.csv\tiris24.csv\n"
     ]
    }
   ],
   "source": [
    "ls data*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm data.tar.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Clean up"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm scripts/The_Unix_Shell_Copy.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rm -r data2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "01_The_Unix_Shell.ipynb\n",
      "01_The_Unix_Shell_Solutions.ipynb\n",
      "The Unix Shell - File and Directory Management.ipynb\n",
      "The Unix Shell - Finding Stuff.ipynb\n",
      "The Unix Shell - Getting Help.ipynb\n",
      "The Unix Shell - Shell Scripts.ipynb\n",
      "The Unix Shell - Working with Text.ipynb\n",
      "data\n",
      "hello.txt\n",
      "one two three\n",
      "scripts\n",
      "stderr.txt\n",
      "stdout.txt\n",
      "test1.txt\n",
      "\n",
      "./data:\n",
      "example.fna\tiris.csv\tiris24.csv\n",
      "\n",
      "./scripts:\n",
      "avg.sh\t\t\tcat_if_exists.sh\textract_headers.sh\n"
     ]
    }
   ],
   "source": [
    "ls -R"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Bash",
   "language": "bash",
   "name": "bash"
  },
  "language_info": {
   "codemirror_mode": "shell",
   "file_extension": ".sh",
   "mimetype": "text/x-sh",
   "name": "bash"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}