Marine Biological Laboratory Workshop on Molecular Evolution  
Marine Biological Laboratory
HomePeopleScheduleSoftwareResourcesForums

Resources
File Formats
Glossary
Hardware
References
Substitution Models
The Amphioxus Song
Converting File Formats
Course T-Shirts
Likelihood Ratio Test
Online Journals
Photo Gallery
Scientific Societies
Tree Formats
UNIX Text Editors
UNIX Tutorial
Using a Laptop at the Workshop


UNIX Text Editors

There are several text editors that create plain text files, such as emacs, vi and pico. Unless you are already familiar with vi or pico, we recommend that you use EMACS (Editor MACroS), known simply as emacs. We strongly recommend that you study the emacs tutorial, which you can easily start in any empty session.

In emacs you use combinations of special keys and character keys to invoke commands. The commands usually involve either the CONTROL key (CTRL or CTL) or the META key (ESC on MAC or ALT, EDIT on others). Therefore, Ctrl-h (or C-h) means that you press the CONTROL and h key together, while Ctrl-h t (C-h t) means that you press the CONTROL and h keys, then release both keys and tap t.

To start the emacs tutorial:

Ctrl-h t

To get help in emacs:

Ctrl-h

To exit emacs, type:

Ctrl-x-c

To exit an emacs command, type:

Ctrl-g

For an emacs Command Summary open this link

Creating and Editing Files

To open and edit a file in emacs, simply type

emacs myfile
(my file can be a new or an existing file)

To save a file:

Ctrl-x-s

To choose a file from the current directory:

Ctrl-x-f
(type '.'-ENTER in dialog box at bottom of window)

To move within your file in emacs:

previous line Ctrl-p

next line Ctrl-n

backward 1 char Ctrl-b

forward 1 char Ctrl-f

backward 1 word Meta-b

forward 1 word Meta-f

To navigate by page and file:

forward one page Ctrl-v

backward one page Meta-v

backward to start of file Meta-<

forward to end of file Meta->


Cut OR Copy & Paste Text

Very Important Command:

Undo last text edit Ctrl-x u


Complete lines of text:

Set cursor position to start of Cut or Copy

Set Mark Ctrl-space-bar

Cut text Ctrl-w

Copy text Meta-w

Reset cursor and paste text Ctrl-y

Blocks of text:

Set cursor position to start of Cut or Copy

Set Mark Ctrl-@

Move cursor across text and down to delineate rectangular area

Cut text Ctrl-x rk

Copy text Meta-x rk

Reset cursor and paste text Ctrl-x ry

To work with two files in two different emacs panes:

Split panes Ctrl-x 2

Move between panes Ctrl-x o

Cut, Copy & Paste as instructed above between 2 files


Replace Text Uniformly

Query for replace text in dialog box (prompt = Query replace: ) Meta-%

tap Enter

type replacement text (prompt = "Query replace with:")

tap Enter

Enter key for number of times to replace
! = replace every instance
space bar or y = replace one instance recursively
n to skip to next, q to exit, period to replace one match and exit
comma to replace but not move point immediately


Create Keyboard Macro

These are recorded keystrokes to automate text editing in emacs.

Start recording macro Ctrl-x (

tap a sequence of keystrokes

End recording of macro Ctrl-x )

Execute last macro in memory Ctrl-x e



Sample file for demonstration:

sample text file
.......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ..........

Maintained by Adam Bazinet
Direct questions and comments to Michael Cummings