Introduction to Bio-Linux

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Nedit Pros: very easy quite intuitive colouring schemes are available for programming syntax Cons: it is an X program (i.e. graphical), and can’t be run from a text-only environment it is (slightly) slower to start up than non-graphical editors Exercise Editing a file with pico In a terminal, type pico. Write some information into this file. Try the options listed at the bottom of the screen. the ^ means the Control key (Ctrl). So, for example, to check the spelling, use Ctrl-t. The command Ctrl-o saves the file and allows you to continue working on it, and Ctrl-x saves the file and exits pico. When you are done, save your file and exit. Editing a file with nedit Type nedit & Type some text into the window. Look under the menus for the kinds of options available to you. Under the Shell menu, try the options wc (word count) and number lines. Save your file under a different name than the one you used for the file you created with pico and exit nedit. Reading text files There are many commands available for reading text files on Linux/Unix. Among the most common are cat, more, and less. cat streams the entire contents of a file to your terminal. It is not generally a good command to use to read files except ones with very little text. cat is a very useful command for concatenating files though! (More on this function later.) more and less are commands that show the contents of a file one page at a time. less has more functionality than more. With both more and less, you can use the space bar to scroll down the page, and typing the letter q causes the program to quit – returning you to your command line prompt. In addition, once you are reading a document with more or less, typing a forward slash / will start a prompt at the bottom of the page, and you can then type in text that is searched for below the point in the document you were at. Typing in a ? also searches for a text string you enter, but it searches in the document above the point you were at. Hitting the n key during a search looks for the next instance of that text in the file. 8
With less (but not more), you can use the arrow keys to scroll up and down the page, and the b key to move back up the document if you wish to. Exercise Read the file hsy14678.embl using the commands cat, more and less. cat hsy14768.embl more hsy14768.embl less hsy14768.embl Use the spacebar to scroll down Press q to quit. Use the spacebar to scroll down, b to go up a page, and the up and down arrow keys to move up and down the file line by line. Press the / key and search for the letters sequen in the file. Press the ? key and search for the letters gene in the file. Press the n key to search for other instances of gene in the file. There are many command line options available for each of the above commands, as well as functionality we do not cover here. To read more about them, consult the manual pages: man cat man more man less Copying and pasting text To select text for copying, press the left mouse button to highlight the text. To paste, you have the window you wish to paste to selected, (usually meaning it is the top window on view), and press the middle mouse button once – if you have a two button mouse, press both buttons simultaneously to emulate the middle mouse button. Exercise Open two terminals. In one, use the command less to open one of the files you created in the previous exercise. Open up another terminal and start pico. Copy and paste text from the first terminal into the window running pico. Save your file (if you want to), and exit pico. 9
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