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Navigating Files/Directories

Changing and Checking Directories

File systems follow a heirarchy. Think of the files in your computer, you have folders which can contain folders or files. Now that have our tutorial data we will enter or change into our unix_tutorial folder or directory with the cd command (cd being short for change directory):

cd unix_tutorial

Now we have entered a directory! But how do we understand where we are? We can do this with the pwd command (print working directory):

pwd

output

~/Documents/unix_tutorial

This output will be a little different for every user based on your computer's file structure. However, you will note here that we are within the root folder (~) which contains all other folders, the Documents folder, and finally the unix_tutorial folder. This string of folders showing where we are is called our file path or just path for short.

Listing Directory Contents

Now this unix_tutorial folder has other folders inside it. We can list these folders with the ls command:

ls

output

data_folder results_folder  scripts_folder

Here we see that we have three folders: data_folder, results_folder, and scripts_folder. If we want more information on our files we can add options to our command. Let's do this by adding the long option to our ls command:

ls -l

output

total 0
drwxr-xr-x  4 username  groupname  128 May 13 09:33 data_folder
drwxr-xr-x  2 username  groupname   64 May 13 09:26 results_folder
drwxr-xr-x  2 username  groupname   64 May 13 09:26 scripts_folder

The long format will usually have 8 columns: - permissions of the file

Permissions

permissions are split into a line of 10 characters. The first character will be a d if it is a directory and a - if it is a file. Then the characters are read in groups of three - the first three characters are the user's permissions, the next three are the group permissions and the last three are other user permissions. r means someone can read the file/folder, x means someone can execute (like as in executing a script), and w means someone can write to the file/folder.

  • number of files (folders count as 2, files count as 1, so for example data_folder has 2 files in it)
  • the username
  • the group name
  • size of the file/folder
  • day of modification
  • time of modification
  • file/folder name

Now let's practice navigating directories by entering our data_folder:

cd data_folder
pwd

output

~/Documents/unix_tutorial/data_folder

To move around we have a few shortcuts. If we want to move to our root folder (where all other folders live) we can use the cd ~ command. To move one folder up we can use the cd .. command:

cd ..
pwd

output

~/Documents/unix_tutorial

References

  1. Introduction to the Command Line for Genomics