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Basic Unix Commands 5: Accessing Content I

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Command Line Tools for Genomic Data Science

Johns Hopkins University

4.2 (291 ratings) | 13K Students Enrolled

Course 5 of 8 in the Genomic Data Science Specialization

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.

Skills You'll Learn

Bioinformatics, Samtools, Unix, Command-Line Interface

Reviews

4.2 (291 ratings)

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WL

Jul 07, 2016

This is perhaps one of the most clearly taught courses I have had on Coursera. Thank you for putting in time to teach us!

GY

Aug 29, 2017

Highly recommended.\n\nI suggest you take it before "Genomic Data Science with Galaxy".

From the lesson

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

Taught By

Liliana Florea, PhD
Assistant Professor

Transcript

In this section we will be looking at Unix commands for

accessing content In files, in directories.

This will also give us an opportunity to explore the content of the files for

the three species for our particular application.

So let's start with apple.

Now all of our files are located in the apple directory so

we're going to change the directory to apple.

One easy way of looking at the content of each file is with a command more.

More apple.genome.

So this will allow us to look at the content of the file one page at a time, or

one line at a time, by pressing Return.

We can also press the Space bar and that will move ahead one full screen.

We'll do this again to demonstrate another option.

You will notice that the genome file has a specific structure.

We call this a file, which is used to represent sequences.

We'll be talking about this in more detail in our following lecture.

A file is represented with one header for each sequence.

In this case, that is marked

with a greater than sign followed by an identifier unique to that sequence.

Here it is chromosome one and

then followed by one are multiple lines of strings.

Over the A, C, D, G alphabet.

Sequences can be quite long and

we might not be able to scroll to the end of the sequence.

So under certain circumstances, we might want to see where the start

of the next sequence in the file is, and we can do so by

with a slash, and then looking for the limiter, the greater than sign.

So these will take us in the file to the location of the next sequence.

The next sequence is named chromosome two, and the sequence itself follows.

And we can repeat this looking for the next sequence.

Chromosome three.

Chromosome four.

Chromosome five.

And then the pattern is not found.

So this is a fast file containing five different sequences.

Chromosome one, chromosome two, chromosome three, chromosome four, and then five.

And we shall call this a multi-fast file.

So that's what the genome file looks like.

We can view the same information.

With a command less.

Less apple.genome.

So it starts from the beginning.

We can recognize chromosome one,

the first sequence followed by this string of nucleotides.

And spacebar will move us forward in the file.

But unlike more, which only allowed us to move forward in the file,

less also allows us to go backward.

So pushing the up arrow would allow us to go backward in the file.

So we can move bidirectionally in this case.

That was the apple.genome file.

We can now use the more and less commands in a similar fashion

to look at the other types of files that we have in this directory.

So let's take a look at the genes file, more apple.genes.

The genes file will contain annotation, which is information about the genes and

where they are located within the general mix sequence.

It is organized in columns, and here for instance in the first column we have

the gene name, in the second column we have the variant.

And that explains a little bit.

The chromosome where it's located, the start location on the chromosome,

end location, whether it's located on the fourth,

or plus, versus the reverse or minus trend of the genome.

And then a string that uniquely characterizes this gene and this variant.

Namely its structure along the genome.

So the gene seen in this particular case might be genes such as smell, size,

color, taste, shape but their might be other genes that

do not correspond to a particular trait or collectively correspond to some traits.

And here those are indicated with appl4, appl5, 8, 9, and 10.

And to think of variance for instance you might think about the color of an apple

as being red, yellow, or green.

We just mark them color one, two and three.

So we use more which allowed us to view the content of the file apple.genes.

Of course we can illustrate with less, and

we will obtain the same information in a similar manner.

Lastly, let's take a look at the last type of files which is apple.samples.

So we will say apple.samples.

And it simply tells us what are the portions of the that

were sampled by a particular experiment, in this case root, leaf, and foot.

We can observe the information in a similar way for the peach and

the pear directories which I am now going to illustrate here.

So more or less are basic commands for accessing content in Unix.

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