Basic Unix Commands 2: Files, Directories, Paths

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En provenance du cours de Johns Hopkins University

Command Line Tools for Genomic Data Science

207 notes

Johns Hopkins University

Command Line Tools for Genomic Data Science

207 notes

Cours 5 sur 8 dans Specialization Genomic Data Science

Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.

À partir de la leçon

Basic Unix Commands

In this module, you will be introduced to command Line Tools for Genomic Data Science

Basic Unix Commands 1: Content Representation3:29

Basic Unix Commands 2: Files, Directories, Paths7:29

Basic Unix Commands 3: File Naming4:00

Basic Unix Commands 4: Content Creation9:28

Basic Unix Commands 5: Accessing Content I6:25

Basic Unix Commands 6: Accessing Content II4:55

Basic Unix Commands 7: Redirecting Content6:10

Basic Unix Commands 8: Querying Content15:43

Basic Unix Commands 9: Comparing Content11:18

Basic Unix Commands 10: Archiving Content13:42

Basic Unix Commands 11: Practical Exercises I13:11

Basic Unix Commands 12: Practical Exercises II9:14

Rencontrer les enseignants

Liliana Florea, PhD
Assistant Professor
McKusick-Nathans Institute of Genetic Medicine

In this section we will be looking at how we represent content in Unix and

some of the basic commands in Unix.

So let's start by opening a terminal.

The way we communicate with the Unix operating system

is via an interpreter or shell.

And we give it commands, and then it responds back if it understands it.

So in this case let's start with some basic Unix commands.

Let's type date, and then it responds with Tuesday, March 24, 2015.

Let's try echo hello, and it echoes hello.

So it understand that particular comment.

Now let's try foo, and the interpreter,

the shell language, does not recognize the command and it says command not found.

So there's a basic language of commands that is being

recognized by the interpreter.

One very useful command is pwd, this print working directory.

And it gives us the current location within the file system.

As you may recall, content is organized into files in the computer,

and the files are themselves located in two directories, which may

be part of other directories, and so on, until we reach the root directory.

So any particular location within the file system can be represented

by its direct path from that location to the root of the system,

which is what we have represented here.

In Unix, every level in the hierarchy is marked by a slash.

So we have a slash here, which represents the root, then the directory users,

then its sub-directory, lilianaflorea, with sub-directory Desktop,

sub-directory Coursera, and then Plants and that's our current location.

We can go from this location or

any other location to any other one in the file system by using the comment cd.

That's change directory.

So, for instance, we can change directory

to /Users/lilianaflorea/Desktop/.

And then we can move on from that location to Coursera/Plants.

As you've noticed, I used two types of referent to get to the directories.

The first type is by using the absolute path

from the root to the current location.

The other way was a relative way of

moving around the file system by moving from the current directory.

So once I was in the current directory, I changed it to its subdirectory,

Coursera, and subdirectory within it is called plants.

There are two special directories for which we have abbreviations.

One of them is the current directory, which is represented as a dot.

And another one is the parent directory which is represented as dot dot.

Before we do so, before we move into the parent directory,

I would like to show you how we can look at the file content and

the directory content within a particular location.

So we are in the directory Plants.

Typing ls, then, will give us a list of all

the files that we have represented in this particular directory.

And as you can see here, we have files that are associated with the tree

species that we mentioned in the previous section, with apple, peach and pear.

We also have a few additional files.

Let's say that we wish to go to the parent directory.

We would use cd.., which represents the parent directory.

Let's see what directory that is.

pwd, print working directory.

And we are in Users/LilianaFlorea/Desktop/Coursera.

Just like before, we can see its file content with ls.

We have a PowerPoint file, the Plants directory that we were in previously, and

an archive.

We want to go back to our Plants directory and we do so with cd Plants.

And then ls will convince us that we're tooling the directory we wish to be in.

So when I'm typing ls, you might notice that the files are listed in

alphabetical order, with files starting with an uppercase character

being listed before files that start with lowercase.

Sometimes we might wish to have additional information about the files and

there are several command line parameters that can be used.

One very useful one is the- l, ls -l would list

additional information about the files.

So you might notice here that each each file is listed with the first digit.

The information as to whether it is a directory or a file.

D here marks a directory whereas the dash marks a file.

Then the set of permissions which we will not cover in this particular section.

Then the number of links to the file, the user name and owner name of the file,

the group that the owner belongs to, the file size in bytes,

the date when it was last modified, and lastly the filename.

As I mentioned, the files are listed in alphabetical order.

A very useful option is to see them in the order in which they were created or

rather, reverse chronological order.

So type in ls -lt in the current directory would

show pear.samples, months, orchard, and so on.

And you can look at the modification type.

You can view other options for these commands and

others at any time by looking at the manual pages, so

man ls would give us the information about the command ls and so on.

So this concludes our first part of the section on how we represent

content in Unix.

For the next section, we will look at how we can handle representing and

listing content when we have a very large number of files.

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