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.
