Introduction to Bio-Linux

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Command history and filename completion (aka. how to cut down on typing!) Using your history A history of the commands you have used is stored as you work. You can access this list and use it to see previous commands, and to re-run previous commands. If you use the up arrow key when you are at the prompt in your terminal, you can see previous commands you have run. This is particularly useful if you have mistyped something and want to edit the command without writing the whole command out again. You can view past commands using the command history. To re-run a command listed by the history command, you can just type the command number, preceded by an exclamation mark. E.g. !268 By default, if you type the command history, you will see the last 15 commands. To see more, just put the number of previous commands you wish to see after a hyphen. For example, to see the last 30 commands, type: history -30 Using filename completion If you type in a command with a filename, and instead of completing the filename, you press the tab key part way through, the system will try to complete the filename for you. If the part of the filename you have written is unambiguous, i.e. there is only one filename that would fit that pattern, the rest of the filename will be filled in for you. If the pattern is ambiguous, all the filenames that match it will be presented to you. You can then choose to type out the full name of the file, continue typing until the pattern is not ambiguous and press tab again, or, instead, if you press tab twice, you will see that the system will cycle through all the filenames that fit your pattern – you can just keep hitting tab until you get to the correct filename. Exercise Type ls hsy and hit the tab key. Type ls test and hit the tab key. Hit the tab key again. Cycle through the filename options given to you. Type history Run one of your previous commands using ! followed by the number of the command. 10
Piping commands – how to make the output of one command be the input for the next There are many instances when you will want to use the output of one command as the input for the next command. For example: what if you wanted to see the last 200 commands you ran? This would scroll of the screen before you could read it. However, if you could take the output from the history command and run it through a command like less, you could view the list page by page. To do this, you need to use the pipe symbol | This is usually found in the bottom left of your keyboard, although on some keyboards, it may be elsewhere. The picture on the keyboard may be a straight line up and down, or it may look like two lines, one on top of the other. To call up the last 200 commands run, and run them through the less command, you would type: history -200 | less Finding patterns with grep An important function in Linux/Unix is grep. If you provide grep with a bit of text, it will search for that text in a file and return any lines that contain that text. By default, grep is case sensitive. Exercise Search the file hsy14768.embl for the term DE. grep DE hsy14768.embl If you give grep the –i parameter, what happens? grep –i DE hsy14768.embl If you want to specify that you only want to see lines that begin with the letters DE, then you can preface them with ^: grep ^DE hsy14768.embl If you only want to see lines that end in UK, you can specify this by using the $ symbol at the end of the text: grep UK$ hsy14768.embl 11
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