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Lecture #3: Working with files

Learning objectives

Unix/Linux Command-line

  1. Copy and move single files and multiple files with cp and mv, respectively
  2. Be aware of the risks when copying and moving files
  3. Delete single files, multiple files, and directories with rm
  4. Be aware of the risks when deleting files
  5. Make symbolic links with ln
  6. Describe when you might want to use a symbolic link
  7. Use wildcards to represent sets of files in commands
  8. Use relative paths in shell commands to access other directories without going to that directory
  9. Combine shell concepts with redirection and pipes

Textbook Reference

Chapter 1, Pages 17-26

Activities

  1. open a terminal

  2. download a new set of sandbox files

  3. unzip those files in your sandbox

  4. find those files in your sandbox

  5. make a directory called hobbies

  6. open a new file named sports.txt in that directory with nano and list some of your favorite sports or other physical activities, either to play or to watch.

  7. cp

    • copy a file with cp sports.txt movement.txt - note: within the same directory

    • explore different patterns for different combinations:

      • one file to new file within this directory (see above)

      • one file to new file with the same name in a different directory

        • mkdir ../memoirs
        • cp sports.txt ../memoirs/.

      • one file to new file with different name in a different directory

        • cp sports.txt ../memoirs/family_sports.txt

      • many files to a different directory, all with the same names

        • mkdir ../family
        • cp sports.txt movement.txt ../family/.

      • many files to a different directory, each with a new name - is this possible?

  8. mv

    • change to the memoirs directory

    • move a file with mv sports.txt movement.txt

    • explore different patterns for different combinations:

      • one file to new file with the same name in a different directory

        • mkdir ../youth
        • mv movement.txt ../youth/.
        • mv ../youth/movement.txt .

      • one file to new file with different name in a different directory

        • mv movement.txt ../youth/sport.txt
        • mv ../youth/sport.txt .

      • many files to a different directory, all with the same names

        • cp sport.txt movement.txt
        • mv movement.txt sport.txt ../youth/.

      • many files to a different directory, each with a new name - is this possible?

  9. rm

    • delete a file with rm movement.txt
    • go up one directory
    • delete the youth directory with rm youth - does this work?
    • try rm -r youth - does that work?

  10. ln

    • return to your hobbies directory
    • edit the file sports.txt in your editor
    • return to your memoirs directory - has the file family_sports.txt changed?
    • delete the family_sports.txt file
    • make a symlink to a the original file with ln -s ../hobbies/sports.txt family_sports.txt
    • open ../hobbies/sports.txt in your editor and change a line = has the file family_sports.txt changed?
    • open family_sports.txt in your editor and change a line - has ../hobies/sports.txt changed?
    • replace both the files in the family directory like this

  11. Flags and wildcards

    • change to the data/elements directory in sandbox files

    • examine the file names - what do you notice?

    • make a listing of all the files and their sizes

    • make a listing of only the files that begin with S with ls S*

      • is it any different if you type ls S*.xml?
      • Use this to determine which vowel is the most common 2nd letter in an element name

    • make a listing of only the files that have a single letter with ls ?.xml

      • make a listing of only the files that have two letters

    • make a new directories parallel to this one called periodic_table_1 and periodic_table_2

    • copy all the 1-letter elements to periodic_table_1 and all the 2-letter elements to periodic_table_2

    • go up to the data directory directory

    • copy the whole north-pacific-gyre directory to make a copies called south-pacific-gyre and north-atlantic-gyre

    • in each copy, delete all the text files in the 2012-07-03 directory

  12. Pipes and redirection

    • It is possible to send the output of one command into the input of another command
    • stdin and stdout
    • go to the data/pdb directory in the sandbox
    • look at the top of lanoxin.pdb using head
    • extract lines 2-4 of lanoxin.pdb using head -n 4 lanoxin.pdb | tail -n 3
    • It is possible to send the output of one command to a file
    • save lines 2-4 of lanoxin.pdb using head -n 4 lanoxin.pdb | tail -n 3 > AUTHOR.txt
    • look at ethylcyclohexane.pdb, determine which lines begin with AUTHOR and append those lines to AUTHOR.txt

  13. history

    • review the history of your commands using history
    • save the last 5 lines of your history to a file using history | tail -n 5 > recent_history.txt

Command-line Cheat Sheet