Unix basic commands

Karen Cristine Goncalves, Ph.D.

2023-01-26

Basics

• Commands are separated by a new line (Enter, Return) or a semicolon (;)
• The first word in a command is what you are asking the computer to do (a function)
• Spaces are used to separate file names, commands, etc.
• Some commands allow you to customize their output with options
  • These are single letters, a word, or several words preceded by - or --
• You can get help for a command by using the help option (either -h , --help ) or the command man (for manual)

ls --help
man ls

About spaces and file names

Put name in quotes if it has spaces (test code below)

touch Programming Class.txt
ls

touch "Programming Class.txt"
ls

Quotes are NORMALLY (not always) interchangeable (test code below)

echo "This is good"
echo 'This is good'

Do not start with one quote type and end with another

Shortcuts - part 1

• ~ or $HOME : your home folder (can be defined by the user)
• . : the folder that you are currently in
• ..: the folder that contains the one you are currently in
• Ctrl+C: cancel a command
• In MobaxTerm, find and modify useful shortcuts by clicking on Settings -> Keyboard shortcuts

Shortcuts - part 2

• whoami
  • prints your username (if saved in the computer)
• Use tab to complete words
• In a current command or in a text file, move the cursor faster by using Ctrl+Arrow (right or left arrow in a command line, in a text file up and down arrow too) (this works everywhere!!!)

Basic commands - part 1

• cd
  • acronym for “change directory” (directory = folder)
  • If used alone, opens your home folder
  • The name of the folder to which you want to go comes after cd
    • cd , cd ~ and cd $HOME are synonyms
  • cd - - takes you to the previous folder

Basic commands - part 2

• pwd
  • acronym for “print working directory” (directory = folder)
  • equivalent to the R function getwd() or python’s os.getcwd()
  • prints the full path to your current folder
  • A full path always starts from the root (/)

Basic commands - part 3

• ls
  • lists the contents of your current folder
  • Check slide 2 where we used this command
• Use > after a command to save the output

pwd > myFolder
cat myFolder

• Use >> to add the current output to a previous file

ls >> myFolder
cat myFolder

Managing text files - part 1

• cat : prints the contents of the file to the screen (check slide 9
  • Do not use it with files are that not text (images, pdfs, compressed files) or is too big
  • If several files names are put after the command, one file is printed followed by the next (conCATenation)
• head and tail: prints to the screen the first/last 10 lines of the file

Managing text files - part 2

• less : opens the file as “read-only”
  • Search for a word in a file inside less by typing “/” followed by the word
  • To close less, press Q
• more : opens the file as “read-only”, when the file is closed, prints it to the screen

Managing text files - part 3

• nano : open a text file to edit it.
• grep : searches for a word/phrase in the file and prints the lines that match
  • Can search for several phrases (one per line) in a file by using the option -f
  • If you don’t care about the upper/lower case, use the option -i or --ignore-case

Managing text files - part 4

Search for lines that have the word programming in the file myFolder created in slide 9

grep "Programming" myFolder

• wc : word count. Counts the number of characters, words and lines in a file
• echo : repeats the text that follows it (check slide 4)

Exercise

• Save a fasta file into your home folder with the name myFasta.fa
• Use grep to find all the lines with sequence IDs.
  • Note - put the word or phrase you will search for inside ""

Exercise - Solution

• Save a fasta file into your home folder with the name myFasta.fa
• Use grep to find all the lines with sequence IDs.
  • Note - put the word or phrase you will search for inside ""

# In all fasta files, the sequence ID line is indicated by the symbol >, so we just need to look for it

grep ">" myFasta.fa

• Normally, if you just search for one word, the quotes are not needed, by in this case, the symbol ">" could also mean “send the output to”, which would replace the myFasta.fa file

Managing files - part 1

• cp : acronym for copy
  • cp file file2 : creates a copy of the file “file” and saves it in the file “file2”
  • cp file folder : creates a copy of the file “file” and saves it with the same name in the folder “folder”
  • cp file file2 folder: both files “file” and “file2” are copied into the folder “folder” with the same names
  • cp folder folder2 -r : the option -r allows the copy of the entire folder.
    • If folder2 doesn’t exist, it will be created to hold the same files as “folder”
    • If folder2 exists, a copy of “folder” will be created inside of folder2

Managing files - part 2

• mv : acronym for move. Move file from one place to another
  • mv file file2 : renames “file” as “file2”
  • mv file folder : moves “file” into the folder “folder”
  • mv file file2 folder: both files “file” and “file2” are moved into the folder “folder” with the same names
  • mv folder folder2 :
    • If folder2 doesn’t exist, it is the same as renaming “folder” as “folder2”
    • If folder2 exists, “folder” is moved to that folder

Managing files - part 3

• rm : acronym for remove. Deletes files. They are PERMANENTELY deleted, there is no trash bin here!!!!!!!
  • rm file file2 : deletes both files
  • rm file file2 -i : asks the user if they really want to delete each file, if y is pressed, the file is deleted (-i for interactive)

Managing folders

• mkdir : acronym for “make directory”. Creates new folders with the specified names.
  • Gives an error if something with the same name already exists in the current folder.
  • If many names are given (separated by spaces, creates all names folders)
• rmdir : acronym for “remove directory”. Deletes empty folders.
  • If the folder is not empty, gives an error.
  • If many names are given (separated by spaces, deletes all names folders if they are empty
• rm -r folder : as in cp, the option -r allows the rm to work with a folder. It deletes everything in the folder, then deletes the folder itself

Resources for help

Glossary of commands

Book on basic unix commands