Bash Commands and Scripts

Commands related to navigating the filesystem

• touch filename.txt will create file
• pwd - print working directory - or - "where am I?"
• ls - list directory contents
• ls -l - long list
  • Everything has three types of permissions
    • Read
    • Write
    • Execute
  • And three groups whose permissions can be controlled
    • Owner
    • Group
    • Others
• Wikipedia on Unix Permissions
• la - list with hidden files
• cd - change directory
  • will accept absolute or relative paths
• chmod - change permissions - specify who (ugo), how (+ or -), and what (rwx)
• man <command> - gives us the manual page and options for any Unix command (q will get out of manual page)
• Notes about command-line navigation

Commands related to files and folders

• cp - copies a file
  • cp originalFile.txt newFile.txt
• mv - moves or renames a file
  • To change location, use paths: mv myFile.txt ./folder/myFile.txt
  • To change name, just use different names: mv myFile.txt newName.txt
• cat filename.txt - view file contents - can be called on multiple files and will conCATenate their contents
  • cat file1.txt file2.txt file3.txt will show all files in command line
  • cat *.txt shows all text in files with the file ending .txt
• ls *.txt show all files that end in .txt
  • ls ../*.txt go up one directory then tell me the txt files there (still within the same directory)
• head -n # - view the first # of lines of a file
• tail -n # - view the last # of lines of a file
• less - view the contents of a file a little at a time nice way to scroll through
• touch filename.txt - quickly create a new file
• nano filename.txt - this is actually an entire text editing program (type text like normal)
  • write out is save and ^=control (^O) exit (^X)
• wc - print out the length of a file in lines, words, and characters

Practice Exercise 1

(1) Create a file with the touch command.
(2) Make a copy of the file using cp.
(3) Rename the original version of the file to something else with mv.
(4) Use nano to add different text to each copy and save it.
(5) View the contents of each file with cat.
(6) Check the sizes of each file with wc.

• echo - prints something to the screen (or elsewhere, as directed)
• >> - appends to file
  • echo "some text here" >> myTextFile.txt
• > - writes to (or over!) file
  • echo "more text here" > myTextFile.txt
• WARNING - BIG WARNING - PAY ATTENTION - rm permanently removes a file
  • No going back - always use this VERY carefully
  • I know people who've accidentally erased their entire computers using this command
  • rm -r recursively removes a directory and everything inside it - even more dangerous than just rm!
  • This is the reason permissions are so important. If someone doesn't have write permissions on a file or folder, they shouldn't be able to delete it.
• mkdir MyDirectory - create a new (empty) directory (folder)
• rmdir MyDirectory - remove an empty directory !!WARNING!!
• wildcards - * is especially useful - matches anything
• grep - find only lines matching some particular string

Practice Exercise 2

(1) Create a series of new text files, with some filenams starting with one letter and some starting with another.
(2) Use echo and output redirection (> or >>) to add content to the files.
(3) With one command, list all the files that start with one particular letter.
(4) Make a new directory
(5) Move all files that start with one particular letter into the new directory.
(6) Try to remove that directory with rmdir. Can you?
(7) Extract all the lines from the files you created that contain one particular word of your choosing.

• Notes about editing files and folders from the command line

Parsing File Contents

Another very powerful command is called awk, which can do lots of different forms of text parsing. For the purposes of this course, we will focus on using awk to extract individual columns (generally separated by spaces or tabs) from a file. The syntax we will use looks like this

awk '{print $1}' test.txt

This will print out the first column. To print the third column, we would use

awk '{print $3}' test.txt

To print both the first and third columns, we could do this

awk '{print $1,$3}' test.txt

Commands related to the Unix environment

• Can create a variable and assign value using =
  • myVariable=2
• Can print value of variable using echo and starting name with $
  • echo $myVariable
• | - the Unix pipe can be used to send the output of one command into the input of another
  • history | tail -n 20 >> endOfHistory.txt
• Can store the output of a command in a variable by first execute the command in backticks

  myVariable=`ls | head -n1`
  

• Note that bash is sensitive to spaces! Don't leave any spaces before or after your equals sign when assigning a value to a variable.

Practice Exercise 3

(1) Create a new variable.
(2) Assign a numeric value to this variable.
(3) Print the value of the variable to the screen.
(4) Print the value of the variable to a new file.
(5) Assign a character or word value to your variable.
(6) Print the value of the variable to the screen.
(7) Append this new value of the variable to the file you created in step (4).
(8) Assign the 4th file or folder name you see when you execute ls to your variable. Use backticks, ls, head, tail, and pipes!
(9) Append the name of this file or folder to your new file.

Practice Exercise 4

(1) Use history, a pipe, tail, and >> to extract the last 50 lines from your command history and store them in a new file (recentCommands.txt).
(2) Open your new file with less and scroll through to make sure the contents are correct.
(3) Use cp to make another copy of this file (recentCommands2.txt).
(4) Make a new folder called myCommands.
(4) Use mv to relocate recentCommands2.txt to your new folder.
(5) Change your working directory to this folder
(6) Open recentCommands2.txt in nano and make some edits. Save your edits and quit nano.
(7) Use cat to view the contents of your edited file and make sure it saved properly.
(8) Use rm recentCommands2.txt to delete this new copy.

You can download a copy of test.txt here.

Introduction to scripts

• What is a script?

  • Fundamentally, a bash script is just a file containing a series of bash commands.
  • Scripts are formatted as text files. But the things in this file are special.
  • The first line of a script file tells the computer in which language (i.e., shell) we're writing our script. This line starts with "#!" - also known as a shebang. The shebang tells Terminal that we're about to indicate which language we're going to use.
  • Follow the shebang with the path to the shell that you'd like to use. Yes, the shell itself is a program!
    • #! /bin/bash
  • Let's start by creating your first script - myScript.sh
    • nano myScript.sh
    • Add the shebang line
    • Add two commands in the body of the file
      • echo "Hello, "$USER"!"
      • echo "I'M A SCRIPT AND I WORK!"

• Scripts contain series of commands

  • This is essentially your first foray into programming.
  • You'll need to think through the steps involved in whatever task you need to complete and then write a command for each step.
  • This ability to break a big problem into individual steps is the most important skill in programming.
  • As an example, let's write a program together to do a basic analysis of a dna sequence. This sequence is already available in the week 5 repository in dnaSequence.txt. This is a real sequence from the human genome (at least, some human genomes) and we'd like to count the number of As, Cs, Gs, and Ts that it contains.

• Command-line Arguments

  • To access the argument from inside the script, bash reserves the special variables $1, $2, $3, ...
  • For practice, go back to myScript.sh that we created earlier and change $USER to $1. Now, run it by typing myScript.sh <YOUR_NAME>

Assignment 3

Will be posted on Jan. 30th