01-UNIX-and-Terminal.ipynb

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    "# Command Line\n",
    "\n",
    "**OBJECTIVES**:\n",
    "\n",
    "- Create, Delete, and Navigate files and directories in the Terminal\n",
    "- Copy and Rename files in the Terminal\n",
    "- Use Pipes and Filters to combine commands in Terminal\n",
    "- Locating Files and things in Files in Terminal\n",
    "\n",
    "\n",
    "Before the advent of the mouse, computers were only able to interact with typed text commands.  There are many advantages to this way of interacting with your machine, we will explore some of these today.  I believe the terminal to be important in terms of the speed you are able to complete operations and the control that you have over these operations.\n",
    "\n"
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    "### Introduction to Shell\n",
    "\n",
    "On a mac, I type `cmd` + `spacebar`, write **terminal** and hit `enter`.  This will bring up a new terminal.\n",
    "\n",
    "- **Navigating Files**\n",
    "\n",
    "  - `cd`: Change directory\n",
    "  - `pwd`: Print Working Directory\n",
    "  - `ls`: List Files\n",
    "  - `ls -F`: List Files with Flag\n",
    "  - `ls -l`\n",
    "  - `ls -R`\n",
    "  - `ls -t`\n",
    "  - `ls -R -t`\n",
    "  - `cd ..`: Move one directory up\n",
    "  - `cd ~`: Move to root directory\n",
    "  \n",
    "  \n",
    "  \n",
    "  "
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    "### Problems\n",
    "\n",
    "1. **Absolute vs Relative Paths**\n",
    "\n",
    "> Starting from `/Users/amanda/data/`,\n",
    "> which of the following commands could Amanda use to navigate to her home directory,\n",
    "> which is `/Users/amanda`?\n",
    ">\n",
    "> 1. `cd .`\n",
    "> 2. `cd /`\n",
    "> 3. `cd /home/amanda`\n",
    "> 4. `cd ../..`\n",
    "> 5. `cd ~`\n",
    "> 6. `cd home`\n",
    "> 7. `cd ~/data/..`\n",
    "> 8. `cd`\n",
    "> 9. `cd ..`\n",
    "\n",
    "2. **Relative Path Resolution**\n",
    "\n",
    "> Using the filesystem diagram below, if `pwd` displays `/Users/thing`,\n",
    "> what will `ls -F ../backup` display?\n",
    ">\n",
    "> 1.  `../backup: No such file or directory`\n",
    "> 2.  `2012-12-01 2013-01-08 2013-01-27`\n",
    "> 3.  `2012-12-01/ 2013-01-08/ 2013-01-27/`\n",
    "> 4.  `original/ pnas_final/ pnas_sub/`\n",
    ">\n",
    "> ![](images/unix/filesystem-challenge.svg)\n",
    "\n",
    "\n",
    "3. **`ls` Reading Comprehension**\n",
    "\n",
    "> Assuming a directory structure as in the above Figure\n",
    "> (File System for Challenge Questions), if `pwd` displays `/Users/backup`,\n",
    "> and `-r` tells `ls` to display things in reverse order,\n",
    "> what command will display:\n",
    ">\n",
    "> ~~~\n",
    "> pnas_sub/ pnas_final/ original/\n",
    "> ~~~\n",
    "\n",
    "\n",
    "> 1.  `ls pwd`\n",
    "> 2.  `ls -r -F`\n",
    "> 3.  `ls -r -F /Users/backup`\n",
    "> 4.  Either #2 or #3 above, but not #1."
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    "### Files and Directories\n",
    "\n",
    "- `mkdir`: Creates directory\n",
    "- `touch`: Creates file\n",
    "- `nano`: Simple text editor in terminal\n",
    "- `rm`: Removes file\n",
    "- `rm -r`: Removes recursively\n",
    "- `rm -i thesis/quotations.txt`: Removes responsibly\n",
    "- `rm -r -i thesis`: Recursive responsibilities\n",
    "- `mv`: Moves a file\n",
    "- `cp`: Copies a file\n",
    "\n",
    "\n",
    "1. **Moving to the Current Folder**\n",
    "\n",
    "> After running the following commands,\n",
    "> Jamie realizes that she put the files `sucrose.dat` and `maltose.dat` into the wrong folder:\n",
    ">\n",
    "> ~~~\n",
    "> $ ls -F\n",
    ">  analyzed/ raw/\n",
    "> $ ls -F analyzed\n",
    "> fructose.dat glucose.dat maltose.dat sucrose.dat\n",
    "> $ cd raw/\n",
    "> ~~~\n",
    "> {: .language-bash}\n",
    ">\n",
    "> Fill in the blanks to move these files to the current folder\n",
    "> (i.e., the one she is currently in):\n",
    ">\n",
    "> ~~~\n",
    "> $ mv ___/sucrose.dat  ___/maltose.dat ___\n",
    "> ~~~\n",
    "\n",
    "\n",
    "2. **Renaming Files**\n",
    "\n",
    "> Suppose that you created a `.txt` file in your current directory to contain a list of the\n",
    "> statistical tests you will need to do to analyze your data, and named it: `statstics.txt`\n",
    ">\n",
    "> After creating and saving this file you realize you misspelled the filename! You want to\n",
    "> correct the mistake, which of the following commands could you use to do so?\n",
    ">\n",
    "> 1. `cp statstics.txt statistics.txt`\n",
    "> 2. `mv statstics.txt statistics.txt`\n",
    "> 3. `mv statstics.txt .`\n",
    "> 4. `cp statstics.txt .`\n",
    "\n",
    "3. **Moving and Copying**\n",
    "\n",
    "> What is the output of the closing `ls` command in the sequence shown below?\n",
    ">\n",
    "> ~~~\n",
    "> $ pwd\n",
    "> ~~~\n",
    "\n",
    "\n",
    "> ~~~\n",
    "> /Users/jamie/data\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    " $ ls\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    "> proteins.dat\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    " $ mkdir recombine\n",
    " $ mv proteins.dat recombine/\n",
    " $ cp recombine/proteins.dat ../proteins-saved.dat\n",
    " $ ls\n",
    "> ~~~\n",
    "\n",
    ">\n",
    "> 1.   `proteins-saved.dat recombine`\n",
    "> 2.   `recombine`\n",
    "> 3.   `proteins.dat recombine`\n",
    "> 4.   `proteins-saved.dat`\n",
    "\n",
    "4. **Organizing Directories and Files**\n",
    "\n",
    "> Jamie is working on a project and she sees that her files aren't very well\n",
    "> organized:\n",
    "\n",
    "> ~~~\n",
    "> $ ls -F\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    "> analyzed/  fructose.dat    raw/   sucrose.dat\n",
    "> ~~~\n",
    "\n",
    ">\n",
    "> The `fructose.dat` and `sucrose.dat` files contain output from her data\n",
    "> analysis. What command(s) covered in this lesson does she need to run so that the commands below will\n",
    "> produce the output shown?\n",
    ">\n",
    "> ~~~\n",
    "> $ ls -F\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    "> analyzed/   raw/\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    "> $ ls analyzed\n",
    "> ~~~\n",
    "\n",
    "> ~~~\n",
    "> fructose.dat    sucrose.dat\n",
    "> ~~~\n"
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    "### Investigating Files\n",
    "\n",
    "- `cat`: Displays file contents\n",
    "- `head`: Displays top rows of file\n",
    "- `tail`: Displays bottom rows of file\n",
    "- `sort`: Allows for different sorting\n",
    "- `wc`: Word Co\n",
    "- `*`\n",
    "- `?`\n",
    "- `command > file`\n",
    "- `first | second`\n",
    "\n",
    "- `grep` \n",
    "- `grep -w`\n",
    "- `grep -n`\n",
    "- `grep -n -w`\n",
    "- `grep -n -w -i`\n",
    "\n",
    "- `find .`\n",
    "- `find . -type d`\n",
    "- `find . -type f`\n",
    "- `find . -name '*.txt'`"
   ]
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   "source": [
    "### Further Reading\n",
    "\n",
    "- Software Carpentry: [**The UNIX Shell**](http://swcarpentry.github.io/shell-novice/)"
   ]
  }
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