Unix Basics Review
|mkdir||make a directory|
|rm||use caution, it is easy to delete more that you would like|
|head||prints the top few lines to the terminal window|
|tail||prints the last few lines to the terminal window|
|sort||sorts the lines|
|uniq||prints the unique lines|
|grep||filnds the lines that contain a pattern|
|wc||counts the number of lines, characters and words|
|date||returns the current date and time|
|pwd||return working directory name|
|scp||remote secure copy|
|~||represents your home directory|
|man [command]||manual page for the command|
Unix Problem Set
- Log into your machine or account.
- Mac Users: Open the application: Terminal
- From Terminal: `ssh -Y email@example.com
- Windows users -- Please refer to the PuTTY instructions with your username and the server
- What is the full path to your home directory?
- Go up one directory?
- How many files does it contain?
How many directories?
Using a text editor create a fasta file and name it sequences.fasta. Make sure it ends up in the proper directory, locally or remotely.
- This is fasta file format:
- Without using a text editor examine the contents of the file sequences.fasta.
- How many lines does this file contain?
- How many characters? (Hint: check out the options of wc)
- What is the first line of this file? (Hint: read the man page of head)
- What are the last 3 lines? (Hint: read the man page of tail)
How many sequences are in the file? (Hint: use grep)
Rename sequences.fasta to something more informative of the sequences the file contains. (Hint: read the man page for mv)
- Create a directory called fasta. (Hint: use mkdir)
- Copy the fasta file that you renamed to the fasta directory. (Hint: use cp)
- Verify that the file is within the fasta directory. (Hint: use ls fasta/)
- Delete the the original file that you used for copying. (Hint: use rm, be careful)
- Read the man page for rm and cp to find out how to remove and copy a directory.
- Print out your history and redirect it to a file called unixBasics.history.txt
Commands to try
You can string more than one command together with a pipe (|) , such that the output of the first command is received by the second command.
ls -lt | head
You can string more than one command together with a semi-colon (;) , such that the commands run sequentially, but that output does not get passed into the next command.
date; some program command ; date
You can redirect the output of a command into a file
grep PATTERN > PATTERN.txt
You can append the output of a command to a file
grep PATTERN2 >> PATTERN.txt
You can redirect stderr to a file
command 2> filename
You can redirect the output (stdout) and stderr to a file
command &> filename