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Basic Unix Commands 7: Redirecting Content

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用于基因组数据科学的命令行工具

约翰霍普金斯大学

4.2（297 个评分） | 13K 名学生已注册

课程 5（共 8 门，基因组数据科学专项课程）

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.

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您将学习的技能

Bioinformatics, Samtools, Unix, Command-Line Interface

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4.2（297 个评分）

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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".

从本节课中

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

教学方

Liliana Florea, PhD
Assistant Professor

脚本

In this section we will be talking about how we can redirect content in Unix.

You may recall that sometimes the output from one command for instance, cat,

can be very large.

Too large for the human mind to be able to see it.

At the speed at which it is displayed.

So, cat */*.genome.

Showing the genome files.

Will only allow us to view the last few lines of the last file.

In Unix, content is organized in files.

And the files are organized in directories.

And the files have a particular location within the directory structure.

However, there are three additional types of files.

Three standard files that are used for input and output.

So these are the standard input, standard output, and standard L.

So, for instances, lets take the command, when we're typing the command cat

apple/apple.genome.

The comment cat takes it's content from the file apple/apple.genome.

Or when we're typing echo hello, the command echo is taking it's input.

Is being, but in this case it's taking its input from the command line.

And namely it's hello.

Let's give one more example of a comment, WC.

WC word count, is another way of accessing the content within a file.

So if we wish to see, for instance, how many lines or

how many characters we have in one file, we can use wc.

wc apple/apple.genome.

Would give us four pieces of information.The

first one will be the number of lines in the file.

The second one will be the number of words in the file.

Recall that each line here was one word.

So it makes sense for the number of words, and the number of lines to be the same.

Then we have the number of characters in the file.

And followed by the name of the file itself.

We can use wc-l to view just the number of lines in the file.

So apple/apple.genome gives us 1083 lines.

In this case, that we see -l

took it's input from the file

apple/apple.genome.

We can redirect files, in standard input into standard output.

For instance, instead typing wc -l apple/apple.genome,

the output was presented to the terminal.

So, there's a standard output.

We can redirect the output using the greater than sign.

Into a file that will give us, for instance, nlines, the number of lines.

So, now the file nlines would show us the output that we

previously saw at the standard output.

And we can do similarly, with the input file with the less than sign.

So for instance we can say wc -l.

And we apply that to the file, apple/apple.genes, and we get 16.

So we can use the greater than

sign to redirect the output from a command line, from the terminal to a file.

And we can use the less than sign.

In order to redirect the standard input from the terminal, to a particular file.

One other redirect operation that is very very useful is the piping.

With this vertical bar.

That essentially takes the output from one program, in the list of commands.

And pipes it to become the input of another program.

So in this case, we will illustrate with, let's say, ls.

Let's show ls, we have one, two, three, four, five, six items.

We type ls.

And then we pipe the output, which would be these six words.

To become the input of the command wc -l.

So this will show six.

And you have seen how the output of one command, becomes the input for

the next command.

Similarly, going back to our command, cat.

We can use the command cat, */*.genome.

Which was appending the call cat.

The content of the three genomes file.

And we can pipe it to the command more.

Which allows us to see it one page at a time.

So this is chromosome one,

spacebar, chromosome two.

Chromosome three, four, five.

And we should soon see scaffold 1, scaffold 2 and so on.

You don't need to go to the next file.

We will see more examples on how to redirect output, and

redirect input in the following section.

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